OBO Foundry Newsletter Issue 10

This issue reports recent decisions of the OBO Foundry Operations Committee, updates from the Editorial and Technical Working Groups, and the current status of ontology submissions under review. It also highlights infrastructure updates and ongoing discussions relevant to the broader OBO community.

The OBO Foundry continues to rely on active community engagement. Contributions through ontology development, issue tracker discussions, working group participation, tool building, and newsletter submissions remain essential to sustaining shared standards and collaborative progress.

OBO Foundry Operations Committee.

Updates

OBO Dashboard updated

The OBO Dashboard was updated (2026-03-18); ontology maintainers should review current compliance status. Ontologies that satisfy the required criteria are listed on the OBO Foundry homepage (https://obofoundry.org). Ontology developers are encouraged to review the dashboard regularly to identify areas for improvement and ensure continued compliance with Foundry standards.

The most recent dashboard status can be accessed via the OBO Dashboard page on the OBO Foundry website. (last updated 2026-03-18) here: OBO Dashboard (2026-03-18)

Decisions Made and Working Group Updates

During the Issue 10 reporting period, the Editorial Working Group and Technical Working Group finalized several documentation updates, policy refinements, and workflow changes. These actions strengthen OBO’s standardization guidance, clarify resolvability requirements, improve submission quality control, and formalize tool lifecycle management.

• Contents of Standardization Guidelines document finalized: The Standardization Guidelines is a document developed to contain suggestions and recommendations deemed too detailed to be included as part of a Principles page. The guidelines currently include (1) Technical Considerations (addressing logical consistency after ontology reasoning, how to indicate ontology root terms, and use of standard synonym types); (2) Content Considerations (addressing preferred sources for imported terms, when to (not) import whole ontologies, and how to use NCIt terms); (3) Release Considerations (addressing the standards for different release types); and (4) Communication Considerations (addressing links to term issues). This document is not yet linked from the OBO Foundry web site, but a pre-release version is available in the Standardization Guidelines draft.

• Principle updates clarifying IRIs and resolvability requirements: Reference to “imported from” was removed from Principle 1. Previously, “imported from” was used to indicate the ontology serving as the direct source of a term import, which could be either the primary (term-maintaining) ontology or an intermediary source. While its use is not prohibited, existing guidance recommending import from the primary source reduces its necessity.

  Principle 3 was strengthened to require that the official ontology PURL, after redirection, MUST resolve to the ontology OWL file, and that PURLs for individual terms MUST resolve to dedicated, term-centric pages. These updates reinforce consistent identifier practices and improve reliability of ontology access across the OBO Foundry.

• Terminology standardization across documentation: Mentions of “OBO Library” have been replaced with “OBO Foundry” across core documentation pages, including the Principles summary page, Principle 3, Principle 12, and the ID policy page. This update standardizes terminology across official guidance.

Ongoing Discussions

• Practice for referring to taxa not in NCBI Taxon (#434): Discussion continues regarding best practices for representing taxa not present in NCBI Taxon. The issue remains open pending further clarification.

AI-related activities in the OBO community

Artificial intelligence is under active discussion within OBO as a potential support mechanism for ontology development and curation workflows.

• OBO Academy sessions on AI-assisted biocuration: In parallel, community-led activities are advancing the application of AI in biocuration and ontology engineering. OBO Academy sessions led by Chris Tabone demonstrated the use of large language models (Claude Code) for ontology development workflows (Part 1: https://youtu.be/pUoelp2qbDI; Part 2: https://youtu.be/UOjzTGnG_XM). These sessions illustrated practical applications, including automated term generation, ontology editing support, and workflow acceleration, while also highlighting challenges related to validation, reproducibility, and integration with existing curation standards.

• AI in biocuration (ISB Virtual Biocuration Conference 2026): A workshop on AI in biocuration (February 9, 2026) demonstrated the use of large language models in curation workflows and knowledge representation (recording: https://youtu.be/jXHmHHLp9q0; details: https://www.biocuration.org/events/biocuration2026-virtual/). The workshop highlighted practical applications for AI-assisted curation, along with challenges related to validation, reproducibility, and integration with established ontology development standards.

• LinkML community discussion on AI governance: A LinkML community call (February 19, 2026) addressed governance considerations for AI use, including discussion of an “AI covenant” and its potential role in defining responsible use of AI in ontology development, documentation, and data integration (recording: https://youtu.be/EOYypShdKdw).

• AI4Curation guidance resources: Community-developed documentation provides guidance for applying AI tools in biocuration and ontology workflows (https://ai4curation.io/aidocs/), supporting more consistent and transparent adoption across projects.

• OBO Slack channels for AI discussions: Two dedicated Slack channels (#ethical-ai, #ai) have been established to coordinate discussion of ethical, technical, and governance considerations related to AI use, indicating increasing community engagement around responsible AI integration.

Ontologies

New Ontologies Accepted in the OBO Foundry Ontology Library

Physiologically Based Pharmacokinetics Ontology (PBPKO)

• GitHub Issue: #2563
• Key Discussion: PBPKO provides structured terminology to support representation of physiologically based pharmacokinetic models and related biological processes. Following review and dashboard validation, the ontology was accepted for inclusion in the OBO Foundry. The submitter has been instructed to complete the required metadata file prior to final issue closure.
• See also: Newsletters 8-9

New ontologies currently under review

Intrinsically Disordered Proteins Ontology

• Status: Under review
• Join the discussion: GitHub Issue: #2770
• Key Discussion: Review has been completed with requested changes; the ontology is awaiting implementation of reviewer feedback before further evaluation.

Precision Fermentation Ontology

• Status: Under review
• Join the discussion: GitHub Issue: #2821
• Key Discussion: PREFER has passed NOR dashboard validation and is undergoing editorial assessment. Reviewer follow-up is pending.

microntology

• Status: Pre-registration incomplete
• Join the discussion: GitHub Issue: #2835
• Key Discussion: Required items in the pre-registration checklist remain incomplete. The submitter has been notified, and review will continue once outstanding requirements are addressed.

Clinical Metadata Exploration Ontology

• Status: Technical corrections required
• Join the discussion: GitHub Issue: #2822
• Key Discussion: Review identified invalid URIs and missing definitions. The submitter has been notified and revisions are required before further consideration.

Spotlight on well-established OBO ontologies

In this issue, we highlight The Ontology of Adverse Events (OAE) from the OBO Foundry family.

The Ontology of Adverse Events (OAE)

The Ontology of Adverse Events (OAE): A Decade of Expansion and a New Milestone.

Launched in 2011 as an OBO Foundry community ontology, the Ontology of Adverse Events (OAE) remains a critical resource for standardizing and integrating data on adverse events (AEs) following medical interventions. A recent publication in Scientific Data (January 2026; PMCID: PMC12917244) documents the ontology’s remarkable evolution over the past decade, highlighting its enhanced role in enabling computational pharmacovigilance and supporting the advancement of precision medicine. Since its last major update in 2014, OAE has undergone a substantial expansion to improve its clinical granularity and domain coverage. The ontology now contains 10,829 formally defined terms — a 251% increase from the 3,086 terms previously reported. The OAE framework now explicitly models critical determinants influencing clinical outcomes, such as administration routes, dosage parameters, and patient demographics (e.g., age), facilitating more nuanced analyses. By mining data from major sources like VAERS and FAERS and integrating with regulatory vocabularies like MedDRA, OAE effectively bridges the gap between raw clinical reports and structured computational analysis. To broaden its utility within the global scientific community, developers have also introduced “Chinese Translation” annotations for new terms, supporting OAE’s applications in monitoring post-immunization adverse events in China. By providing a logically structured and interoperable platform for adverse event representation, OAE continues to empower cross-disciplinary analysis of adverse event patterns, etiological factors, and outcome trajectories, ultimately fostering safer medical interventions and advancing translational research.

Updates on well-established OBO ontologies

MONDO (Mondo Disease Ontology)

The Mondo Disease Ontology is now available within Epic Electronic Health Record (EHR) systems through integration with IMO Health’s terminology platform. As part of Epic’s February 2026 software update, health systems using IMO Core can document diagnoses using Mondo-linked terms directly in clinical workflows.

IMO Health has mapped nearly 5,000 new rare disease diagnoses and aligned more than 25,000 existing clinical terms to standardized Mondo identifiers. This integration enables clinicians to continue using familiar terminology while ensuring that documentation is connected to unified, computable Mondo IDs behind the scenes.

The expansion significantly improves rare disease representation in clinical systems. Coverage of rare genetic disease diagnoses increases from 51% to 75% compared to ICD-10 alone, while maintaining greater than 99% precision. Research conducted at Cincinnati Children’s further demonstrated that enhanced terminology support identified 5.5 times more rare diseases and 20% more patients than standard ICD-10 coding alone.

Embedding Mondo into routine clinical documentation strengthens the alignment between research-grade disease definitions and point-of-care workflows. Structured capture of rare disease data supports improved cohort identification, clinical trial matching, longitudinal analysis, and downstream analytics, including artificial intelligence applications that depend on standardized, high-quality clinical data.

Members and Volunteers

The OBO Foundry is honored to highlight valued community members in each issue. This time, we feature Valerie Wood and Shawn ZK Tan.

Valerie Wood

Valerie Wood is Project Manager of PomBase (www.pombase.org), the comprehensive knowledgebase for Schizosaccharomyces pombe, a widely used model eukaryote. She has over 30 years of experience in fission yeast biocuration, beginning with genome sequence feature annotation and subsequently expanding into ontology-driven curation of molecular functions, genetic and physical interactions, phenotypes, and, more recently, GO-CAM pathway models.

Val has been a major contributor to the development of the Gene Ontology since its inception. She also maintains the Fission Yeast Phenotype Ontology (FYPO), originally developed by Midori Harris, and contributes regularly to several community ontologies, including Mondo Disease Ontology, the Sequence Ontology, and ChEBI (Chemical Entities of Biological Interest).

She recently published a perspective article titled “Empowering Biological Knowledgebases: Advances in Human-in-the-Loop AI-Driven Literature Curation” (DOI: 10.1093/bioadv/vbag028), with colleagues from the ELIXIR Biocuration Focus Group. This work reviews how artificial intelligence (particularly large language models) is being applied to support literature curation, outlines key challenges, and provides practical recommendations for future development.

PomBase is actively integrating AI into its biocuration workflows, including the use of ai4curation tools developed by Chris Mungall and colleagues to accelerate ontology development, as well as exploring AI-based approaches for extracting ontology-driven annotations from the literature.

Shawn ZK Tan

Shawn is the citizen technology lead in GSK Asia Research & Development and works as an independent consultant operating under his own consulting practice, SignaMind. Shawn has also been part of the OBO Foundry Operations Committee since 2022. Starting his career as a lab scientist, Shawn only started work on biomedical ontologies after his PhD when he joined EMBL-EBI under David Osumi-Sutherland as an ontology editor, developing an ontology to support the data coming out from single cell mapping of the brain. During his time at EBI, Shawn actively contributed to the Cell Ontology (CL), Uberon, the Phenotype And Traits Ontology (PATO), and the Relation Ontology (RO). After his time at EMBL-EBI, Shawn joined Novo Nordisk first as a Senior Research Data Steward embedded in both research projects and ontology development. He subsequently took up a role as a Business Capability Lead where he drove the development and operationalisation of the ontology strategy. During his time at Novo Nordisk, Shawn was a strong advocate for using OBO Foundry ontologies and tools in industry, and for industry taking a bigger role in supporting the OBO community, embedding tools into pipeline and writing about the mutual benefits that exist in such a relationship. In his current roles, he continues advocating for the use of open standards and tools in industry and aims to be a strong advocate for Asia’s data for global use, with ambitions to build up communities and representation in Asia for such purposes. After experiencing the challenges of fragmented data across modern organizations and how they tend not to get the most out of using bio-ontologies, Shawn also started a consultancy, SignaMind, which focuses on helping organizations build up their semantic capabilities, and doing so with strong business value in mind. With SignaMind, he is currently working with The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition (BRIGHT) to build up their semantic capabilities, starting with an ontology for precision fermentation (PREFER).

Spotlight on Research and practice in the OBO community

“Curate This!” Podcast Series Launched by ISB

International Society for Biocuration (ISB) has launched a new podcast series titled “Curate This!”, hosted by Susan Bello and featuring contributions from Charlie Hoyt.

The series highlights perspectives from the biocuration community, exploring the people, practices, and evolving challenges that shape knowledge representation in the life sciences. Topics include ontology development, curation workflows, interoperability, and community infrastructure.

The podcast provides an accessible platform for discussing both practical and conceptual aspects of biocuration, with relevance for ontology developers, knowledge engineers, and data integration specialists across the OBO ecosystem.

The inaugural episode is available on YouTube

The DO-KB knowledgebase 2026 update: expanding programmatic and language access

This recent article reports the 2026 update of the Human Disease Ontology Knowledgebase (DO-KB) in Nucleic Acids Research (Database Issue). Baron et al. describe substantial expansion in disease representation together with major upgrades to programmatic access and multilingual delivery (published online 26 November 2025; Issue 6 January 2026). The update strengthens interoperability through an OpenAPI (OAS 3.1) compliant API, an expanded and reorganized SPARQL Sandbox (now 55 queries with pagination and federated examples), and enhanced cross-resource mappings using structured match designations and SSSOM outputs.

A central contribution is internationalization: the Disease Ontology implemented language tags across labels, definitions, and synonyms and released Spanish-language ontology artifacts alongside bilingual website navigation. This work provides a practical model for multilingual delivery within the OBO ecosystem. The article also documents governance-through-practice improvements aligned with OBO operational priorities, including a clinician-led nosology education program that feeds curated updates back into the ontology and infrastructure modernization (e.g., Neo4j upgrade) to improve performance, sustainability, and long-term accessibility.

Figure from Baron JA, Sánchez-Beato Johnson CM, Schor MA, Olley D, Nickel L, Felix V, Bello SM, Greene C, Lichenstein R, Bisordi K, et al. The DO-KB knowledgebase 2026 update: expanding programmatic and language access. Nucleic Acids Research. 2026;54(D1):D1425–D1436. https://doi.org/10.1093/nar/gkaf1213

Epilepsy disease classification: a community effort to enhance the Mondo Disease Ontology

This recent article reports a community-driven effort to improve the representation and classification of epilepsy within the Mondo Disease Ontology. Vasilevsky et al. describe a series of expert-led workshops that aligned Mondo’s epilepsy hierarchy with the International League Against Epilepsy (ILAE) classification, resulting in substantial revisions to disease structure, terminology, and classification logic (published 16 February 2026). Updates include the addition of new epilepsy types, reclassification of syndromes and etiologies, refinement of hierarchical relationships, and extensive updates to synonyms, definitions, and cross-references to improve clinical relevance and interoperability.

A central contribution is the integration of clinical and ontology expertise to produce a more granular and standardized framework for epilepsy representation. The revised structure supports flexible annotation across levels of diagnostic specificity and improves data integration across resources. The work also highlights ongoing challenges, including defining epilepsy syndromes, distinguishing disease from phenotype, and modeling genetic and temporal aspects of disease. These updates strengthen Mondo’s role in supporting rare disease research, clinical decision-making, and data harmonization across platforms such as RDCA-DAP and ClinGen, while establishing a foundation for continued community-driven refinement.

Figure from Vasilevsky N, Gehrke S, Mullen K, Barua S, Braun I, Brünger T, Coughlin C II, Ivaniuk A, Korn D, Lal D, Marsh S, O’Loughlin E, Olson D, Shwetar Y, Sofocleous C, Vogel-Farley V, Grabenstatter H, Haendel M, Mungall C, Toro S. Epilepsy disease classification: a community effort to enhance the Mondo Disease Ontology. Database. 2026;2026:baag004. https://doi.org/10.1093/database/baag004

ChEBI: re-engineered for a sustainable future

This recent article, “ChEBI: re-engineered for a sustainable future,” describes a full modernization of the Chemical Entities of Biological Interest (ChEBI) database and ontology, motivated by the growing maintenance burden of its legacy infrastructure. Malik et al. report a complete overhaul of ChEBI’s platform database, website, web services, and submission tooling—to improve sustainability, scalability, and long-term operability for a global user base (published online 28 November 2025; Issue 6 January 2026). Key infrastructure changes include migrating from Oracle to PostgreSQL, containerized deployment via Kubernetes, and redesigned web interfaces built for responsive use and improved discovery.

The update also improves programmatic and user-facing access to ChEBI content by replacing legacy SOAP services with modern REST APIs (with interactive Swagger UI documentation), upgrading text search from Lucene to Elasticsearch, and updating chemical structure search to RDKit-based tooling (including dedicated support for substructure and similarity workflows). For ontology and data quality, the release introduces standardized identifiers and relationships (including broader alignment with OBO Relation Ontology), adds new export formats such as OBO JSON Graph, and applies ROBOT-based QC checks—reducing legacy ontology errors and improving consistency of metadata and annotation properties.

Figure from Malik A, Arsalan M, Moreno C, Mosquera J, Félix E, Kizilören T, Muthukrishnan V, Zdrazil B, Leach AR, O’Boyle NM. ChEBI: re-engineered for a sustainable future. Nucleic Acids Research. 2026;54(D1):D1768–D1778. https://doi.org/10.1093/nar/gkaf1271

Spotlight on Research: Now Published

Several research papers previously featured in the OBO Newsletter as preprints have now been published in journals.

The Ontology of Adverse Events in 2025

This recent article reports substantial updates to the Ontology of Adverse Events (OAE), an OBO Foundry ontology designed to standardize and integrate adverse events associated with medical interventions. The work focused on expanding clinical representation, improving semantic structure, and strengthening interoperability to support computational analysis across biomedical domains.

Over the past decade, OAE has expanded from 3,088 terms to more than 10,800 formally defined terms, reflecting significant growth in domain coverage and clinical granularity. New content includes detailed representation of patient anatomic regions, clinical manifestations, and pathological processes, with terms derived from sources such as VAERS, FAERS, MedDRA, and published studies. The ontology also captures key determinants influencing adverse event outcomes, including administration routes, dosage parameters, and demographic variables, enabling structured analysis of clinical and epidemiological patterns.

Interoperability has been strengthened through integration with existing ontologies and knowledge bases, including alignment with BFO as an upper-level ontology and mapping to resources such as the Human Phenotype Ontology, Uberon, and Gene Ontology. OAE supports the development of domain-specific extensions, such as drug- and disease-specific adverse event ontologies, and enables semantic integration across pharmacovigilance datasets and biomedical knowledge systems.

Infrastructure and annotation practices have also been refined. Standardized annotation schemas ensure consistent use of labels, definitions, and metadata, while tools such as OntoFox, OntoBee, and OntoRat support ontology development and reuse. Internationalization efforts include the introduction of Chinese translations and broader adoption in global research contexts, particularly in China’s biomedical data infrastructure initiatives.

Together, these developments position OAE as a comprehensive and interoperable framework for representing adverse events, supporting pharmacovigilance, precision medicine, and cross-domain data integration within the OBO ecosystem.

Figure from Chenchen Pan, Qiuyue Yang, Xue Zhang, Shuyue Luo, Yongqun He, Jiangan Xie. The Ontology of Adverse Events in 2025. 2026 January 13. https://doi.org/10.1038/s41597-026-06584-x

Spotlight on OBO Principles

Principle 8: Documentation

To ensure transparency, traceability, and long-term sustainability, OBO Foundry ontologies must provide clear and comprehensive documentation. Principle 8 requires ontology owners to document the full ontology life cycle and to address multiple audiences, including users and developers. Documentation serves as an indicator of ontology quality and is expected to evolve alongside the ontology, including updates and release records as the resource matures.

Documentation should cover several complementary areas. Global ontology documentation includes metadata describing the ontology as a whole, such as creators, maintainers, license, and version information. Local ontology documentation addresses representational units (classes and relations), including justification of metadata elements, explanation of axiomatization, and clarification of whether textual definitions are manually authored or generated using patterns or software assistance. User documentation should describe the ontology’s purpose, scope, intended use cases, and access methods, potentially including SPARQL query examples, training materials, tutorials, publications, and recorded presentations. Developer documentation should outline contribution workflows (e.g., via a CONTRIBUTING.md file), licensing terms, version control practices, release procedures, deprecation and conflict resolution policies, batch term submission processes, continuous integration, interaction with orthogonal resources, and the use of automated agents for quality control and maintenance.

Implementation requirement: If a term originally defined in ontology A is adopted into ontology B with a new identifier, the annotation assertion rdfs:isDefinedBy MUST be added to record provenance.

In OWL (Turtle serialization), this is expressed as:

<http://purl.obolibrary.org/obo/A_123> rdfs:isDefinedBy <http://purl.obolibrary.org/obo/b.owl> .

In OBO format, this is expressed as:

property_value: isDefinedBy http://purl.obolibrary.org/obo/b.owl

This requirement ensures traceability of adopted terms across ontologies.

Validation: Principle 8 is automatically validated through the OBO Dashboard. Documentation presence and completeness are assessed as part of overall ontology soundness evaluation.

Open considerations include clarifying minimal required metadata, defining minimal documentation thresholds, and articulating the role of peer-reviewed publications in satisfying documentation expectations.

For more details, see the OBO Foundry documentation on Principle 8.

Spotlight on Tools: Recent updates

• Retirement of [funowl](https://github.com/Harold-Solbrig/funowl): The funowl library has been officially retired. A migration guide has been published to support users in transitioning to alternative tooling. This formal retirement clarifies maintenance expectations and helps prevent reliance on unsupported infrastructure.
• Ontology Development Kit (ODK) minor 1.6.1 release with various tool updates
• ROBOT 1.9.10 release with updates to obographs format, prefix injections into OBO format files, a global –input-format option to avoid cycling through all possible parsers with the OWL API and more.

Events and News

Updates on past events

Core Ontology for Biology and Biomedicine (COB) Workshop (January 26, 2026)

The workshop reviewed progress in COB implementation across the OBO Foundry and identified key barriers to adoption. Reported challenges included uncertainty around required COB imports, lack of clear criteria for full COB alignment, and dependencies on RO relations not represented in COB. Planned actions include improving COB documentation, clarifying release artifacts for alignment, and defining alignment standards for ontologies at different stages of development. Coordination between RO and COB was identified as a priority for future work.

Upcoming events

Conferences at ISMB 2026 (Washington, DC)

Three ontology-relevant meetings will be held in July 2026:

• Bio-Ontologies and Knowledge Representation (BOKR) – July 13–14
• Bioinformatics Open Source Conference (BOSC) – July 14–15
  • A joint BOKR/BOSC session will be held for half a day.
  • Abstracts on open-source approaches to knowledge representation may be submitted to either track via ISMB EasyChair.
  • Deadline for talk/poster abstracts: April 9 (not expected to be extended).
  • In-person presentation is required unless a medical or caregiver exemption applies.
• International Conference on Biomedical Ontology (ICBO) – July 13–18
  • Workshops and tutorials are expected during the first part of the week.
  • Submission details are pending clarification.

Biocuration 2026 (Virtual)

• The 2026 Virtual Biocuration Conference Series brings together biocurators, database developers, data scientists, and the broader research community in an accessible and flexible format.
  • More info: https://www.biocuration.org/events/biocuration2026-virtual/

Workshops with Upcoming Deadlines

• ESWC 2026 (Dubrovnik, Croatia, May 10–14)
  • Workshop: LLMs and Knowledge Graphs (LLM4KGOE)
  • Invited speakers are being sought (not funded; registration and travel required).
  • Deadline: February 24 (may be extended).
• ICHI 2026 (Minnesota, USA, June 1–2)
  • Workshop: Food and Health Knowledge Graphs Using Large Language Models (LLMs)
  • Short and long papers will be published in the proceedings.
  • Deadline: March 15.
  • Invited speakers are welcome (not funded).

OBO Academy: Seminar Series (ongoing)

The OBO Academy Seminar Series, organized by members of the Monarch Initiative and open to all, is active again after the summer break. The series offers training and discussions on ontology-related tools and practices. To join, please reach out in the OBO Slack channel #obo-academy.

Upcoming seminars:

• None planned at this time.

The full schedule and materials are available at https://oboacademy.github.io/obook/courses/monarch-obo-training/

You can also vote for or request new training topics at https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace.
• OBO Foundry RSS feed at https://obofoundry.org/feed.xml
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be instead added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• Suggest content for our next newsletter
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are many ways in which you can contribute, including assisting with the production of this newsletter.

Over the past two years, this newsletter has reported on community progress, revisions to OBO principles, and developments in shared infrastructure. In this issue, we present updates from the working groups, highlight recent ontology submissions that have been recently accepted or are still undergoing review, and share recent research and tools that strengthen the OBO ecosystem.

The OBO Foundry depends on active community participation. We encourage you to contribute through ontology development, tool building, raising issues, joining discussions, and proposing content for the next newsletter!

OBO Foundry Operations Committee.

Highlights

OBO Dashboard updated

The OBO Foundry Dashboard tracks how well ontologies follow OBO Foundry principles. Ontologies that meet these principles are listed on the OBO Foundry homepage https://obofoundry.org. We encourage ontology developers to check the dashboard regularly to monitor and improve their work.

You can view the most recent dashboard update (last updated 2025-10-07) here: OBO Dashboard (2025-10-07)

Decisions Made and Working Group Updates

The following updates were approved by the Editorial and Technical Working Groups:

• Proper use of the metadata tag “term tracker item” (IAO:0000233): Values should be restricted to URLs/IRIs, not free text. This ensures clear links between terms and their corresponding tracker items.
• New properties in OMO:
  • “preferred label for community” (OMO:0002001) is a way to denote a synonym / alternative term for a class (or property) to be preferred by some specific community. For example, in the disease community, different groups prefer to talk about the exact same disease using different labels.
  • “has ontology hierarchical property” (OMO:0003014) is a way to document in your own ontology how (based on which properties) you wish hierarchical browsers like OLS and Ontobee to render the hierarchy. Most browsers render rdfs:subClassOf by default, but many ontologies use other properties like “part of”.
• The Editorial Working Group (EWG) is putting together a document that will contain suggestions and recommendations for ontology development for cases deemed too detailed to be a standalone Principle or even to be included as part of a Principles page. The document will include guidelines covering technical considerations, content suggestions, release artefacts, and communication best practices. Thus far, the following guidelines are slated for inclusion:
  • Ontology root term annotation
  • Proper use of the metadata tag “term tracker item”

Other topics will be added as well (see Ongoing Discussions, below).

Ongoing Discussions

• Minimal ontology-level metadata fields (#1365): Discussion surrounds which metadata fields must or should be included in the ontology header section, such as ontology title, description, license, and others. Particular focus is on the use of dcterms:date for cases were semantic versioning (e.g. v1.1.0) is used.
• Ontology root term annotation (#2149): Allows ontologies to specify ontology-specific root terms, helping browsers display hierarchies more clearly.
• Minimal ontology-level metadata fields (#1365): Two tables will be prepared:
  • one with required and recommended fields;
  • one with additional potential fields (including those not to use) with guidance.
• Language tag guidance (#479): There is an increasing interest in having OBO ontologies ‘internationalized’ by including, at a minimum, synonyms in other languages. There is an emerging consensus that xsd:string should be omitted for rdfs:label and IAO:0000115. Further discussion is needed on tooling support, default language tags, and consistency across translations.

These items will continue to be revisited in future meetings as progress is made.

Ontologies

New Ontologies Accepted in the OBO Foundry Ontology Library

Exercise Medicine Ontology (EXMO)

• GitHub Issue:#2615
• Key Discussion: EXMO provides standardized terms for exercise physiology, training interventions, performance assessment, and health outcomes related to physical activity. Following review, the ontology was approved for inclusion in the OBO Foundry with consensus and no objections raised.
• See also: Newsletters 8.

New ontologies currently under review

Physiologically Based Pharmacokinetic Modelling Ontology (PBPKO)

• Join the discussion: GitHub Issue: #2563
  Key Discussion: PBPKO aims to capture concepts used in physiologically based pharmacokinetic modeling. The ontology has undergone multiple rounds of updates in response to feedback. The most recent submission includes modifications that require reviewer follow-up. The review process remains open until these are assessed.
• See also: Newsletter 7.

Experimental Measurements, Purposes, and Treatments Ontology (EMPTY)

• Status: Awaiting updates from submitter
• Join the discussion: GitHub Issue: #2753
• Key Discussion: The ontology proposes to cover experimental measurements, study purposes, and treatment interventions. Initial review identified significant overlap with existing OBO resources. The submitter has requested additional time to revise the scope and address reviewer feedback.
• See also: First introduced in Newsletter 9.

Intrinsically Disordered Proteins Ontology (IDPO)

• Status: Under Review
• Join the discussion: GitHub Issue: #2770
• Key Discussion: The ontology defines concepts and relationships describing the structural states, transitions, and functional roles of intrinsically disordered proteins (IDPs) and regions (IDRs). These proteins lack stable tertiary structures and play key roles in processes such as transcription, translation, signaling, and cell division. The ontology aims to provide a standardized vocabulary to support data integration, annotation, and analysis in structural and molecular biology.
• See also: Newly submitted for review.

A Foundational Ontology for Computational Sociology (OCS)

• Status: Under Review
• Join the discussion: GitHub Issue: #2771
• Key Discussion: The ontology formalizes core sociological concepts and their relationships to support computational social science research. It includes over 700 classes, 250 object properties, and 200 causal relations, all mapped under the Basic Formal Ontology (BFO 2020) framework. OCS enables systematic knowledge representation, automated reasoning about social phenomena, and semantic interoperability across disciplines.
• See also: Newly submitted for review.

Spotlight on well-established OBO ontologies

In this issue, we highlight the Evidence and Conclusion Ontology (eco) from the OBO Foundry family.

Evidence and Conclusion Ontology

Accurate interpretation and reproducibility of scientific conclusions require that every statement or assertion made by a researcher or automated tool be based on supporting evidence that can be shared with, and examined by, the wider scientific community. The Evidence and Conclusion Ontology (ECO) provides terms for the consistent and computable capture of types of evidence used to support scientific statements. ECO began in the early days of the Gene Ontology consortium as a place to contain not only the Gene Ontology evidence codes, but also the wider set of evidence terms in use by the various model organism databases that were part of the consortium. Since then, ECO has grown into an independent ontology used by more than 60 prominent data resources including UniProt and the Alliance of Genome Resources (AGR). Currently ECO contains >2000 active terms encompassing both experimental and computational types of evidence. We continuously add new terms to the ontology in response to requests from our users. Some areas of recent development include terms for machine learning methods developed in collaboration with UniProt, EBI, and AGR as well as terms to describe methods in immune epitope assays in collaboration with the Immune Epitope Database (IEDB). In future work, we will continue to support our existing users, broaden the ECO user community, and integrate ECO with other related ontologies.

Updates on well-established OBO ontologies

Glycosylation Gets a Makeover in the Gene Ontology

The Gene Ontology (GO) recently completed a major revision of its representation of protein glycosylation, particularly N-linked glycosylation (issue #30595). Over time, this branch had accumulated inconsistencies, for example, definitions that included references to arginine and tryptophan N-glycosylation lacking substantial evidence or specific only to bacteria.

The restructuring aligns GO with current biochemical understanding that N-glycosylation primarily occurs via asparagine residues within the Asn-X-Ser/Thr motif, where a preassembled dolichol-linked oligosaccharide is transferred either co- or post-translationally.

The revised hierarchy now distinguishes:

• ER-based glucose/mannose trimming (newly added)
• Golgi apparatus mannose trimming (name updated for clarity)
• N-glycan diversification pathways
• Keratan sulfate proteoglycan biosynthesis (new branch recognizing N-linked vs O-linked variants)

This overhaul involved 8 rounds of discussion and touched 18+ metabolism-related issues. Several of these changes required careful annotation review (go-annotation issues #5827, #5829, #5847, #5859), impacting over 100 experimental annotations across multiple groups. The annotation work involved migrating annotations from obsoleted terms to more specific replacements, reviewing InterPro and Unirule mappings, and ensuring consistency across databases. This demonstrates the collaborative process of modernizing GO to match current glycobiology while maintaining annotation quality.

ChEBI 2.0 redesign

The ChEBI team has launched ChEBI 2.0, a redevelopment of the Chemical Entities of Biological Interest ontology and database. The release updates the entire platform; from infrastructure to user interface; while maintaining data continuity and ontology stability.

Key updates:

• New infrastructure: Rebuilt on modern technologies (PostgreSQL, Django, Vue, Kubernetes) with search powered by Elasticsearch and RDKit.
• Ontology and data products: All downloadable files (ontology, TSVs, SDF, PostgreSQL dump) are now standardized and available at https://ftp.ebi.ac.uk/pub/databases/chebi
• APIs: Legacy SOAP services are deprecated. Users should migrate to the new REST APIs for programmatic access.
• Submission portal: Redesigned and migrated to new backend with improved user management.
• Continuity: All identifiers remain stable and data continue to be released under CC BY 4.0.

Why it matters:

The previous ChEBI codebase had reached its limits. ChEBI 2.0 introduces a simplified schema, faster search, and a scalable foundation for future enhancements; ensuring ChEBI remains a key ontology and data resource for chemical biology.

Milestone:

As of October 2025, the legacy ChEBI website and data releases have been officially retired. Read the full announcement on the ChEMBL blog (See Newsletter 5)

Members and Volunteers

The OBO Foundry is honored to highlight valued community members in each issue. This time, we feature Alexander Diehl.

Alexander Diehl

Alexander Diehl is an Associate Professor at the University at Buffalo. Following training in wet lab molecular biology and immunology and a few years in the biotech industry, Alex joined Mouse Genome Informatics at the Jackson Laboratory in 2003 as a scientific curator and began doing Gene Ontology annotation and development. He has been a project leader of the Cell Ontology since 2005, and has contributed to or developed a number of other biomedical ontologies including the Infectious Disease Ontology, the Ontology for General Medical Sciences, the Neurological Disease Ontology, the Magnetic Resonance Imaging Acquisition and Analysis Ontology, the Cholangiocarcinoma Ontology, and the Ontology for Dental-Care Related Fear and Anxiety. Alex served on the ImmPort and HIPC Data Standards Committee for several years and has served on the OBO Operations Committee since 2018. Alex also teaches undergraduate and graduate courses and mentors students at all levels in Biomedical Informatics at the University at Buffalo, which he joined in 2010.

Spotlight on Research in the OBO community

Expanding and refining the mammalian phenotype ontology to enhance disease model discovery

This recent article highlights major updates to the Mammalian Phenotype (MP) Ontology, an OBO Foundry resource central to disease model discovery. The work focused on expanding disease-relevant terms, improving alignment with the Human Phenotype Ontology (HPO), and strengthening infrastructure for interoperability.

In the past decade the ontology has added over 2,800 new terms including; 140 new terms for pediatric disease models, most notably in congenital heart disease; 124 terms for COVID-19, including diffuse alveolar damage and cytokine storm; and 32 Alzheimer’s-related terms such as amyloid isoform and brain lesion phenotypes. To improve cross-ontology integration, more than 1,500 MP-HPO mappings were created or refined using the SSSOM standard, resolving inconsistencies in labels, definitions, and logical axioms.

Infrastructure and tooling updates further aligned MP with OBO Foundry standards. These included adoption of standardized metadata (ORCID identifiers, date formats), incorporation of uPheno design patterns for logical definitions, and use of ROBOT and the Ontology Development Kit (ODK) for editing, quality control, and release management. Community-facing tools were also strengthened: a new MP-HPO match tool was added to the Human-Mouse Disease Connection (HMDC), and internationalization efforts introduced British spellings and Japanese translations (thanks to the efforts of the MP Japanese Translation Project ).

Together, these developments expand the scope of the MP Ontology and reinforce its alignment with the OBO ecosystem, supporting variant prioritization, disease model discovery, and translational research.

Figure from Susan M. Bello, Anna V. Anagnostopoulos, Leigh C. Carmody, Nicolas Matentzoglu, Cynthia L. Smith. Expanding and refining the mammalian phenotype ontology to enhance disease model discovery. 2025 September 18. https://doi.org/10.1242/dmm.052385

Navigating open-source waters: the pharmaceutical industry’s role in bioontology development

A recent open-access article by OBO Ops member Shawn Tan highlights how the pharmaceutical industry can play a greater role in sustaining OBO ontologies and tools.

This perspective examines how the pharmaceutical industry relies on bioontologies for data integration, FAIR compliance, and AI applications, while development and maintenance remain largely community-driven. The authors identify opportunities for industry to contribute to public efforts, with emphasis on the role of the OBO Foundry and its ecosystem:

• Contributing to ontology content: OBO Foundry ontologies such as Uberon and the Cell Ontology are widely used but resource-constrained. Industry users are encouraged to report issues, propose changes, and contribute pull requests directly to OBO repositories, reducing duplication of in-house fixes and improving interoperability.
• Supporting open-source tooling: OBO Foundry tools such as the Ontology Development Kit (ODK), ROBOT, OAK, and SSSOM provide standardized workflows for ontology management. Active contribution to these tools sustains their development and aligns internal pipelines with community standards.
• Connecting with the community: The OBO Foundry community offers structured entry points (GitHub repositories, OBO Slack, operations committee participation). Engagement enables industry teams to align with ontology development practices, influence standards, and support shared resources such as the Pistoia Alliance’s Pharma General Ontology, which leverages OBO ontologies and LinkML.

Using Novo Nordisk Research & Early Development (R&ED) as a case study, the authors demonstrate how structured engagement with OBO Foundry ontologies and tools can enhance both industry workflows and community resources. They conclude with a call to action for pharma to contribute to the sustainability of open bioontology development.

Mondo: Integrating Disease Terminology Across Communities

The Mondo Disease Ontology is a unified, open-source framework designed to integrate heterogeneous disease terminologies used in research and clinical care. It harmonizes content from 21 disease resources, including OMIM, Orphanet, MeSH, and NCIt, to resolve differences in scope, structure, and naming conventions that limit interoperability and data integration.

Mondo represents approximately 100,000 source concepts as more than 25,000 distinct disease entities encompassing both human and non-human diseases. It includes over 110,000 synonyms, categorized as exact, narrow, broad, or related, following SKOS standards. Each disease entry contains provenance linking definitions and synonyms to original sources.

The ontology supports a pluralistic classification that allows diseases to have multiple parent terms, representing clinical, biological, and genetic perspectives. Logical design templates, Dead Simple OWL Design Patterns (DOSDP), and automated quality control ensure consistent structure and terminology. Mondo’s synchronization workflow imports and aligns updated data from external resources monthly, using a combination of automated matching and manual curation.

Mondo provides curated semantic mappings among major terminologies and distributes these in standardized formats such as SSSOM. Integration with other ontologies, including Uberon, Gene Ontology (GO), and NCBI Taxonomy, links disease terms to anatomical systems, biological processes, and causal organisms. Mondo is used by ClinGen, Open Targets, NORD, OMIM, and MedGen to support consistent disease representation across biomedical databases and clinical applications.

Community contributions are managed through GitHub, where users can propose new terms, report issues, and review changes. More than 5,000 pull requests and 3,900 issues have been recorded since 2017.

Figure: Portion of Mondo disease hierarchy showing several MYH7-related diseases and whether they are recorded in several major databases. This figure shows how Mondo reconciles these diseases, highlighting subclasses of the term “peroxisomal disease” (MONDO:0019053).

Figure from Nicole A Vasilevsky et al., Mondo: Integrating Disease Terminology Across Communities. Genetics, 2025 October 6. https://doi.org/10.1093/genetics/iyaf215

Chemical classification program synthesis using generative artificial intelligence

This article in Journal of Chemical Informatics introduces the ChEBI Chemical Classifier Program Ontology (C3PO), a novel approach that leverages generative artificial intelligence to create explainable Python programs for chemical structure classification in the ChEBI ontology. Unlike deep learning models that often lack interpretability, C3PO produces deterministic classifiers with natural language explanations for each decision.

The method follows an iterative workflow, Learn–Execute–Iterate–Adapt (LEIA), in which large language models generate candidate classifiers that are refined against benchmark data until they reach acceptable accuracy. Results show strong performance for classes with clear structural patterns, such as glycerol-based lipids, while more complex or ambiguous categories remain challenging. Although deep learning systems like Chebifier outperform C3PO in overall accuracy, the program synthesis approach provides complementary strengths in explainability and curator-guided refinement.

This work highlights how AI-assisted program synthesis can support ontology development and chemical database curation. By combining symbolic, rule-based methods with machine learning, future systems may achieve both transparency and accuracy, advancing sustainable classification in ChEBI and related resources.

Figure from Christopher J. Mungall, Adnan Malik, Daniel R. Korn, Justin T. Reese, Noel M. O’Boyle & Janna Hastings. Chemical classification program synthesis using generative artificial intelligence. Journal of Cheminformatics volume 17, Article number: 152. 2025 October 1. https://doi.org/10.1186/s13321-025-01092-3

Spotlight on Research: Now Published

Several research papers previously featured in the OBO Newsletter as preprints have now been published in journals.

SeMRA (Semantic Mapping Reasoning and Assembly), “Assembly and reasoning over semantic mappings at scale for biomedical data integration”, featured in issue 8 has been accepted for publication in Bioinformatics (DOI: 10.1093/bioinformatics/btaf542). The paper presents a framework for assembling, validating, and reasoning over large-scale semantic mappings to improve interoperability across biomedical datasets.

DRAGON-AI (Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence), featured in issue 4, now published in Journal of Biomedical Semantics (DOI: 10.1186/s13326-024-00320-3). The paper describes a framework that applies retrieval-augmented generation methods to support the automated creation and refinement of ontologies, integrating AI techniques with ontology engineering workflows.

SPIRES (Structured Prompt Interrogation and Recursive Extraction of Semantics), featured in issue 4, accepted for publication in Bioinformatics (https://doi.org/10.1093/bioinformatics/btae104). The paper presents a method that uses zero-shot learning and structured prompting to extract and organize semantic information for automatically populating knowledge bases.

O3 Guidelines (Open Data, Open Code, and Open Infrastructure) featured in issue 3, now published in Scientific Data (DOI: 10.1038/s41597-024-03406-w). The paper outlines best practices for ensuring sustainable, transparent, and reusable scientific resources through open data, open code, and open infrastructure.

Artificial Intelligence Ontology (AIO) featured in issue 5, now published in Applied Ontology (DOI: 10.1177/15705838241304103). The paper, “The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies” presents the LLM-assisted construction of AI concept hierarchies for an ontology of artificial intelligence.

Change Language for Ontologies and Knowledge Graphs featured in issue 6, now published in Database (DOI: 10.1093/database/baae133). The paper, “A change language for ontologies and knowledge graphs”, presents a formal language for representing and managing changes in ontologies and knowledge graphs.

Unified Phenotype Ontology (uPheno) featured in issue 6, now published in Genetics (DOI: 10.1093/genetics/iyaf027). The paper, “The Unified Phenotype Ontology: a framework for cross-species integrative phenomics,” presents a framework for integrating phenotype data across species to support comparative and translational research.

Spotlight on OBO Principles

Principle 7: Relations

To ensure interoperability and logical consistency across OBO Foundry ontologies, existing relations must be reused whenever possible. The Relations Ontology (RO) serves as the primary source for standard relations. By reusing RO terms, ontologies enable automated reasoning, detection of inconsistencies, and inference of new knowledge across domains. When a required relation is not available in RO, developers are expected to search other OBO ontologies before introducing a new one. Relations intended for broader use should be submitted to RO. If a relation is retained within a local ontology, it must be defined as a sub-property of an appropriate RO parent relation, if it exists.

Validation: Each relation that does not use an RO IRI is automatically checked. If a relation label matches one in RO but does not use the correct RO IRI, it is flagged as an error. Any other non-RO relations are reported as information messages. This validation is implemented in the OBO Dashboard to support consistency across ontologies.

Coordination with RO is encouraged through GitHub or the OBO Slack #relation-ontology channel.

For more details, see the OBO Foundry documentation on Principle 7

Spotlight on Tools: Recent updates

Protégé

A new version of the Protégé ontology editor, version 5.6.8, was released in September: https://github.com/protegeproject/protege-distribution/releases/tag/protege-5.6.8

It fixes a bug that, depending on the ontology being edited, could cause frequent complete freezes when browsing the ontology, particularly on MacOS.

Events and News

Registration for the International Conference on Biomedical Ontology (ICBO 2025) is now open:

ICBO 2025 is also accepting submissions for short talks of 10–15 minutes. Submissions should be one-page abstracts and are due by October 24, 2025. Acceptance notifications will be sent on October 30, 2025. These talks are intended to support collaboration with the ICBO community and provide an opportunity for feedback on ongoing work. Abstracts can be submitted through the CMT system: https://cmt3.research.microsoft.com/ICBO2025/Track/6/Submission/Create.

For questions, please contact Asiya Yu Lin (ontology.world@gmail.com).

OBO Academy: Seminar Series (ongoing)

The OBO Academy Seminar Series, organized by members of the Monarch Initiative and open to all, is active again after the summer break. The series offers training and discussions on ontology-related tools and practices. To join, please reach out in the OBO Slack channel #obo-academy.

Upcoming seminars:

• November 11, 2025: Generating SPARQL Queries with ChatGPT (Trish Whetzel)
• December 9, 2025: Efficient Biocuration and Bioinformatics with Claude Code Part 2 (Chris Tabone)

The full schedule and materials are available at https://oboacademy.github.io/obook/courses/monarch-obo-training/

You can also vote for or request new training topics at https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace.
• OBO Foundry RSS feed at https://obofoundry.org/feed.xml
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be instead added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• Suggest content for our next newsletter
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are many ways in which you can contribute, including assisting with the production of this newsletter.

In this edition, we highlight the recent approval of Principle 19 (Stability of Term Meaning), which sets critical standards for preserving semantic consistency across OBO ontologies. This milestone provides the community with guidance on maintaining the identity of terms and mitigating semantic drift over time. We also provide updates from the OBO Dashboard, recent decisions by the Operations Committee, and progress made by the Editorial and Technical Working Groups.

We report on the continued revision of Principle 7 (Relations), which manages criteria for allocating relation terms to the Relation Ontology (RO) or domain-specific ontologies. Additionally, this issue reviews several ontology submissions that are under active consideration or technical review.

Our spotlight series features the Relation Ontology (RO) and Unified Phenotype Ontology (uPheno), alongside community-contributed research on semantic interoperability and cross-species phenotype integration.

As always, we encourage you to participate in the OBO community, whether through contributions, feedback, or development efforts.

OBO Foundry Operations Committee.

Highlights

OBO Dashboard updated

The OBO Foundry Dashboard helps track the progress of ontologies in aligning with OBO Foundry principles. Ontologies that meet these standards are featured on the OBO Foundry homepage at https://obofoundry.org. We encourage all ontology developers to regularly consult the dashboard to assess and enhance their ontologies.

You can view the most recent dashboard update (last updated 2025-05-29) here: OBO Dashboard

Decisions Made and Working Group Updates

This period saw continued progress by the Editorial and Technical Working Groups, alongside several key decisions by the OBO Operations Committee. The Editorial Working Group (EWG) received formal approval and publication of Principle 19 (Stability of Term Meaning), which sets forth best practices for versioning and maintaining consistent ontology releases. The EWG also improved Principle 12 (Naming Conventions) by clarifying when term corrections can occur without triggering obsoletion, promoting more consistent terminology across OBO ontologies.

Ongoing Discussions

The Editorial Working Group is currently revising Principle 7 (Relations), which covers the placement of relationship terms across domain-specific ontologies and the Relation Ontology (RO). Committee members are debating criteria such as whether both the domain and range of a relation must exist in the same ontology, and whether logical invertibility is a practical requirement. The goal is to provide clearer guidance for ontology developers while maintaining flexibility across disciplines. A draft revision is in progress, but no consensus has yet been reached. Join the discussion

Ontologies

New Ontologies Accepted in the OBO Foundry Ontology Library

Biomarker Ontology (BMONT)

• GitHub Issue: #2604
• Key Discussion: The Biomarker Ontology provides terms relevant to identifying and describing biological markers in health and disease contexts. The submitter engaged in active feedback resolution and coordinated with the developers of the Ontology of Biological and Clinical Investigations (OBCI) to align future relation modeling. A key point of discussion was whether approval could be granted based on the commitment to update relations once OBCI terms are integrated into the Relations Ontology (RO). The committee agreed that this commitment was sufficient, and the ontology was approved after a public comment period with no objections.

New ontologies currently under review

Physiologically Based Pharmacokinetic Modelling Ontology (PBPKO)

• Status: Reviewer response required
• Join the discussion: GitHub Issue: #2563
• Key Discussion: See Newsletter 7.

Radiation Therapy Ontology (RTO)

• Status: Reviewer assigned; domain expert still needed
• Join the discussion: GitHub Issue: #2683
• Key Discussion: The Radiation Therapy Ontology (RTO) provides standardized terms for radiation procedures, equipment, dosages, and treatment planning. While it passed most of the technical review, it did not comply with Principle 3 due to the use of non-OBO-compliant IRIs. The committee clarified that a valid namespace must be in place at submission. A reviewer has been assigned, but a domain expert is still needed to complete the evaluation.

Experimental Model Ontology (EXMO)

• Status: Resubmitted; in technical review
• Join the discussion: GitHub Issue: #2615
• Key Discussion: The Exercise Medicine Ontology (EXMO) aims to support personalized exercise prescriptions by standardizing terms related to physical activity, health status, and exercise interventions. While recent updates corrected identifier formatting and addressed several reviewer concerns, issues remain with reuse of out-of-scope terms that should be imported from existing OBO ontologies, such as CMO and DOID. Additional revisions are needed to improve modeling of clinical measurements, consistency in axioms for exercise equipment, and completeness of term definitions. The reviewers acknowledged substantial progress and requested the submitter document future term requests to external ontologies. The review remains open while these refinements are implemented.

Spotlight on well-established OBO ontologies

In this issue, we highlight two ontologies from the OBO Foundry family, the Relation Ontology (RO) and the Unified Phenotype Ontology (uPheno).

The Relation Ontology (RO) was designed to classify and organize relationships between entities in the life sciences and biomedicine. Each RO relation is uniquely identified by a Uniform Resource Identifier (URI) and comes with additional information like a human-readable label, synonyms, and definitions, which can be reused in ontologies and databases. RO includes both general-purpose relations, such as part of, and more specific relations applicable to particular domains. Its core relations (“RO Core”) are defined using the domain-independent from the Basic Formal Ontology (BFO) or the Core Ontology of Biology and Biomedicine (COB). RO provides precise semantics for its relations, defining features such as Transitivity, Symmetry, and Inverses. This allows the use of deductive reasoners to infer new relationships and detect inconsistencies. RO is enshrined as the standard ontology for relationship types in the OBO community. The reuse of RO relations is important for maintaining ontology interoperability. Currently, over 140 OBO Foundry ontologies use RO. RO is used across diverse biological and biomedical domains, including neuroscience, mechanistic modeling, environmental sciences, anatomy and development, phenotypes and diseases, and biomedical investigations. It is also used in various databases and knowledge graphs, such as the Virtual Fly Brain. Beyond the OBO ecosystem, RO properties are used in Wikidata, where there are currently 20 Wikidata properties linked to RO properties via the property “Relations Ontology ID” (as of 2021). These properties are used in 13,167,119 statements with ‘in taxon,’ ‘part of,’ ‘located in,’ and ‘has part’ used more than a million times each. The Biolink Model also uses predicates mapped to RO. RO is publicly available on GitHub https://github.com/oborel/obo-relations. Monthly editors meetings are open to the community, more information can be found here.

The Unified Phenotype Ontology (uPheno) brings together various species-specific phenotype ontologies to enable cross-species analysis of phenotype data. The twelve participating ontologies span from vertebrates to single-cell organisms. The focus so far has been on phenotypic changes induced by genetic and environmental manipulations of organisms (Fig. 1), as this is the focus of the participating ontologies. To facilitate the integration of these ontologies, the uPheno working group has developed a library of patterns that can be used to generate standardized terms, including term labels, synonyms, and text and logical definitions. The framework also helps bootstrap entirely new ontologies (e.g., XPO, PLANP, ZP). These patterns have been adopted by the member ontologies to create new terms and/or manage logical definitions for existing terms. At the Biocuration conference in April, we held a workshop to discuss how to improve integration and enhance the upper-level structure of uPheno to increase usability. uPheno currently integrates 12 species-specific ontologies and offers SSSOM-formatted cross-species mappings (e.g., between HPO and MP). This supports critical use cases such as disease gene discovery and variant prioritization, powering tools like Exomiser and the Monarch Initiative.

The ontology files and patterns are all available on the uPheno GitHub site (https://github.com/obophenotype/upheno). The working group meets monthly to discuss issues, please contact info@monarchinitiative.org to receive an invitation. In addition, there is a #upheno channel in the OBO-Community Slack and a dedicated uPheno Slack workspace.

Read more about uPheno in the 2025 Genetics publication: https://doi.org/10.1093/genetics/iyaf027.

Figure 1. uPheno brings together species-specific ontologies within a common framework to facilitate translational research (from https://doi.org/10.1093/genetics/iyaf027).

Members and Volunteers

The OBO Foundry is honored to highlight two valued community members.

Lynn Schriml

As PI of the Disease Ontology project (http://www.disease-ontology.org/) a NIH/NHGRI-funded Genomic Resource and Knowledgebase, established in 2003, Lynn has been active in the OBO Foundry since 2008. She currently contributes to the OBO Operations team, reviewing ontologies, representing the OBO Foundry at conferences, and has previously worked on the OBO Editorial Working Group.

As an Associate Professor at the University of Maryland School of Medicine, her research includes the classification of standardized descriptors of biomedical concepts. She has been involved with the development of a suite of OBO Foundry biomedical ontologies including the Human Disease Ontology, Symptom Ontology, Influenza Ontology, Pathogen Transmission Ontology, Disease Drivers Ontology, and has contributed to the GAZ geographic location gazetteer and the ENVO environment ontology.

A key component of her ontology development has involved ongoing engagement with disease-specific research communities and ontology developers (e.g., Model Organism Databases – drosophila, zebrafish, mouse, rat, yeast and worm, Human Phenotype Ontology, Mammalian Phenotype Ontology, Alliance of Genome Resources) to include extension, revisions and additions to the Disease Ontology based on disease models defined by the research community.

Bjoern Peters

Dr. Bjoern Peters is a Professor at the La Jolla Institute for Immunology in San Diego, California. Since starting his Ph.D. in theoretical biophysics at Humboldt University in Berlin, Germany, he has worked on the development and validation of machine learning tools to analyze and predict which parts of a pathogen, allergen, or cancer cell are targeted by immune responses. Identifying these specific molecular targets of immune responses, called epitopes, recognized by diseased individuals opens a path toward developing diagnostics, vaccines, and therapeutics.

In 2004, he moved to the La Jolla Institute as a postdoc and later became the bioinformatics lead of the Immune Epitope Database (IEDB; PI: Alessandro Sette), which catalogs epitope recognition data curated from the literature. The desire to capture data for the IEDB in a compatible fashion with other databases brought him into contact with the OBO community, and he teamed up with multiple other researchers working on standardizing data capture from a broad range of experimental techniques. This led to the founding of the Ontology of Biomedical Investigations (OBI) in 2006, which he continues to be heavily involved in.

Beyond OBI, Dr. Peters has contributed to many OBO ontologies, the OBO Foundry, and its transition to an ‘operations-driven-project’. He co-led the OBO-services grant with Dr. Chris Mungall and co-initiated the COB project that aims to develop an integration ontology layer for OBO ontologies below BFO. Beyond the IEDB, Dr. Peters has utilized the OBO data standardization techniques for multiple other public-facing database projects as well as for data capture and analysis for data generated in the experimental part of his lab.

Spotlight on Research in the OBO community

Suggestions for extending the FAIR Principles based on a linguistic perspective on semantic interoperability

This article explores the FAIR Guiding Principles emphasize making data Findable, Accessible, Interoperable, and Reusable, yet they do not extensively define the concept of semantic interoperability. In a recent publication, Vogt et al. examine this gap from a linguistic perspective, underscoring the importance of shared understanding for both humans and machines to interpret data effectively.

The authors introduce an enhanced model of semantic interoperability that differentiates between terminological and propositional interoperability, analogous to how language users comprehend words and sentences. They contend that merely aligning terminologies is insufficient; instead, data should be structured like language, with consistent syntax, semantics, and common background knowledge to facilitate reliable interpretation and utilization by humans and machines.

To advance the FAIR framework, they propose enhancements, which they refer to as progressing toward FAIR 2.0, such as developing a comprehensive FAIR ecosystem comprising services for terminology management, schemas, and operational procedures inspired by linguistic models that support meaningful communication.

This interdisciplinary research connects ontologies, linguistics, and data science, highlighting that achieving true interoperability requires establishing shared linguistic and digital understanding.

Figure from Lars Vogt, Philip Strömert, Nicolas Matentzoglu, Naouel Karam, Marcel Konrad, Manuel Prinz, Roman Baum. Suggestions for extending the FAIR Principles based on a linguistic perspective on semantic interoperability. 2025 April 24; https://doi.org/10.1038/s41597-025-05011-x

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

BioPortal is not new (it was first released in 2008), but a new publication highlights recent additions to its functionality. BioPortal (https://bioportal.bioontology.org), developed by the National Center for Biomedical Ontology (NCBO), is the world’s most comprehensive repository of biomedical ontologies. It aims to disseminate biomedical knowledge through principled ontologies, ensuring semantic interoperability across the research landscape.

BioPortal automatically indexes all OBO Foundry ontologies (among others), monitoring them daily and reloading them upon detecting updates. While the OBO Foundry serves as a registry, BioPortal enhances usability by offering a browsable interface and downloadable ontology files (where licensing permits). As of March 2025, BioPortal hosts 1,549 ontologies (1,182 public), representing over 15 million classes and more than 101 million cross-ontology mappings. Its services support a vibrant community, with 18,000+ registered users and over 159 million API calls monthly.

Key features for OBO users include:

• Ontology Browsing and Search: Advanced search tools and collection filters allow intuitive access to OBO and other biomedical ontologies.
• Detailed Ontology Summaries: Each ontology has a dedicated page with metadata, version history, usage metrics, reusable views, and associated projects.
• Class Exploration: Hierarchical class browsing with improved usability.
• Cross-Ontology Mappings: Automatically generated mappings visualize how terms are used across ontologies.
• Annotation Services: The Annotator and Annotator+ services identify ontology terms in text, with support for negation detection.
• REST API: Extensive programmatic access enables integration with external systems like EHRs, decision support tools, and text mining platforms.
• Knowledge Graph Support: KG-BioPortal uses the Biolink Model to merge and query ontologies as a unified knowledge graph.

A standout capability is BioPortal’s interface for suggesting ontology edits. Using the Knowledge Graph Change Language (KGCL), user-submitted changes are converted into GitHub issues, streamlining curator workflows.

BioPortal’s infrastructure supports the broader OntoPortal Alliance, with additional portals serving domains like agriculture and ecology. Looking ahead, BioPortal plans to enhance knowledge graph features, improve metadata (FAIR-aligned), expand mapping support (including SSSOM), and integrate LLMs for smarter annotation.

Figure from Jennifer Vendetti , Nomi L Harris , Michael V Dorf , Alex Skrenchuk , J Harry Caufield , Rafael S Gonçalves , John B Graybeal , Harshad Hegde , Timothy Redmond , Christopher J Mungall , Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. 2025 May 13; https://doi.org/10.1093/nar/gkaf402

Assembly and reasoning over semantic mappings at scale for biomedical data integration

A challenge in the automated integration of biomedical data and knowledge is the heterogeneous usage of ontologies and databases that assign their own identifiers to the same or related concepts. Resolving these overlaps requires high availability and coverage of semantic mappings. However, available mappings are incomplete and fragmented across individual resources, motivating their large-scale integration and processing. Therefore, the authors developed the Semantic Mapping Reasoning Assembler (SeMRA), a software tool with the following components:

1. A high performance object model for semantic mappings (based on SSSOM)
2. A provenance model for automatically generated mappings
3. A confidence model granular at the curator-level, mapping set-level, and community feedback-level
4. Functionality for assembling, reasoning over, and inferring semantic mappings at scale

SeMRA represents mappings as a directed graph and applies inference algorithms such as inversion, mutation, and transitivity to infer new connections between concepts while tracking provenance and confidence. Its modular design enables import from standard formats (e.g., OBO, OWL), custom sources (e.g., OMIM, ChEMBL), and additional plugins, with all references validated against the Bioregistry. SeMRA includes a web application for interactive exploration, quality control, and curation, and supports export in SSSOM and Neo4j formats. The authors demonstrated SeMRA first by aggregating 43.4 million mappings from 127 sources that jointly cover identifiers from 445 ontologies and databases that they made available on Zenodo (https://doi.org/10.5281/zenodo.11082038). Second, they also demonstrated how SeMRA can be configured with a declarative specification and create five domain-specific mapping sets for anatomical terms, cells/cell lines, genes, protein complexes, and diseases (see https://github.com/biopragmatics/semra/tree/main/notebooks/landscape). Their meta-analysis showed that the integration and inference of domain-specific mappings resulted in meaningful consolidation of redundant terms, especially for the disease and protein complexes. Notably, they reproduced and extended the analysis on the disease landscape presented by Haendel et al., 2020 in “How many rare diseases are there?” (https://doi.org/10.1038/d41573-019-00180-y) to incorporate more disease resources.

Figure from Charles Tapley Hoyt, Klas Karis, Benjamin M. Gyori. Assembly and reasoning over semantic mappings at scale for biomedical data integration. 2025 April 16; https://www.biorxiv.org/content/10.1101/2025.04.16.649126v1.full

The Cell Ontology in the age of single-cell omics (PREPRINT)

Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types - forming a core component of a wide range of platforms and tools. In this paper, we describe the wide variety of uses of CL in these platforms and tools and detail ongoing work to improve and extend CL content including the addition of transcriptomically defined types, working closely with major atlasing efforts including the Human Cell Atlas and the Brain Initiative Cell Atlas Network to support their needs. We cover the challenges and future plans for harmonising classical and transcriptomic cell type definitions, integrating markers and using Large Language Models (LLMs) to improve content and efficiency of CL workflows.

Figure from Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian Aevermann, Alida Avola, James P Balhoff, Ismail Ugur Bayindir, Jasmine Belfiore, Anita Reane Caron, David S Fischer, Nancy George, Benjamin M Gyori, Melissa A Haendel, Charles Tapley Hoyt, Huseyin Kir, Tiago Lubiana, Nicolas Matentzoglu, James A Overton, Beverly Peng, Bjoern Peters, Ellen M Quardokus, Patrick L Ray, Paola Roncaglia, Andrea D Rivera, Ray Stefancsik, Wei Kheng Teh, Sabrina Toro, Nicole Vasilevsky, Chuan Xu, Yun Zhang, Richard H Scheuermann, Chirstopher J Mungall, Alexander D Diehl, David Osumi-Sutherland. The Cell Ontology in the age of single-cell omics. 2025 June 10; https://arxiv.org/abs/2506.10037

Spotlight on OBO Principles

Principle 19: Stability of Term Meaning

Principle 19 of the OBO Foundry emphasizes that the meaning of a term must remain stable over time. Specifically, the *referents *the real-world entities a term denotes must not change as a result of edits to its definition or logical axioms. If a proposed change would shift what the term refers to, a new term with a new IRI and definition must be created instead. This helps protect users from semantic drift and ensures that both humans and machines can rely on the identity and consistency of ontology terms.

The principle allows minor edits for grammar or clarity, as long as these do not alter the referent. It also outlines best practices for handling term obsoletion when meanings change significantly, including when definitions become too vague, inaccurate, or misaligned with scientific understanding. Developers are encouraged to provide replacement guidance and consider the impact on downstream users.

For implementation, the principle specifies exact steps for obsoleting terms in OWL and OBO formats, including use of owl:deprecated, replacing logical axioms, and adding structured metadata like replaced_by or consider. All obsolete term labels must be prefixed with “obsolete ” (lowercase and space included) to comply with Principle 12 (Naming).

The adoption of Principle 19 marks an important milestone for the OBO Foundry. It provides a robust standard for semantic versioning and long-term reliability of ontologies. We encourage all ontology maintainers to read the full principle and begin applying its guidance in their workflows to strengthen trust and usability across the community.

Spotlight on Tools: Recent updates

ROBOT v1.9.8

The ROBOT ontology toolset (v1.9.8), released recently, introduces functional improvements relevant to OBO Foundry ontology developers. The update includes new features, library upgrades, and a series of bug fixes.

New functionality includes:

• A –clean-obo option for the convert command, supporting format cleanup.
• Interpolation of ontology and version IRIs within annotation values.
• Support for selecting punned entities using the remove and filter commands.
• Extensions to the template system allowing predicate-object pair specification.

Library and command updates:

• Apache POI upgraded for improved Excel processing.
• Newline-separated value handling added via SPLIT=\n.
• The reduce command now retains SubObjectPropertyOf axioms.

Bug fixes address:

• Output stability and memory use in owl-diff.
• Exclusion of deprecated terms in lowercase_definition checks.
• Improved handling of axiom annotations during merges.
• Clarified template behavior regarding non-ROBOT columns.
• Resolution of subproperty redundancy detection (issues #1014, #1208).
• Support for embedded default queries in JARs.
• Correction of merging behavior for annotated and unannotated axioms.

The release is available on GitHub and includes three downloadable assets.

Feedback and bug reports: https://github.com/ontodev/robot/issues

Ontology Development Kit (ODK) v1.6:

The ODK is a toolbox and workflow system to manage the ontology lifecycle. After more than a year of work since the last major release, version 1.6 has been published on the 29th May.

This version of the ODK adds major new capabilities, including:

• A redesigned update_repo command for easier repository upgrades
• A new ROBOT plugin with commands for efficient subsetting and upper ontology alignment checking.
• Significant improvements in user management in the interplay with docker.
• Many improvements in the executable workflows (“Makefile”), making them faster and more resilient.
• Ability for SQLite/SemSQL format export, for use with tools like the Ontology Access Kit.
• A new test checks the validity of ID policy files, and another ensures ontologies are aligned with upper-level ontologies when configured.
• Better support for managing SSSOM mapping sets, including merging and selective publishing.
• Tooling improvements including new utilities like jinjanate (replacing j2cli), dicer-cli for ID range management, scala-cli (replacing Ammonite), and yq-mf for YAML/JSON/XML processing. Updates to ROBOT, SSSOM, KGCL, LinkML, and other key packages round out this feature-packed release.

Feedback and bug reports: https://github.com/INCATools/ontology-development-kit/issues

curies v0.10.13:

curies is a python based package for managing IRI-curie conversions. An extension to the curies.Converter class that can apply pre-and post-process rules to CURIEs and URIs was added in v0.10.13. For more information about Curies see Newsletter issue 2. A tutorial is available at https://curies.readthedocs.io/en/latest/preprocessing.html

• An extension to the curies.Converter class that can apply pre-and post-process rules to CURIEs and URIs was added in v0.10.13. A tutorial is available at https://curies.readthedocs.io/en/latest/preprocessing.html

import curies
from curies import PreprocessingRules, PreprocessingConverter, PreprocessingRewrites

rules = PreprocessingRules(
    rewrites=PreprocessingRewrites(
        full={"OBO_REL:is_a": "rdfs:subClassOf"},
    ),
)

converter = curies.get_obo_converter()
converter = PreprocessingConverter.from_converter(
    converter, rules=rules,
)

>>> converter.parse_curie("OBO_REL:is_a")
ReferenceTuple('rdfs', 'subClassOf')

• A hook for standardizing local unique identifiers was added in v0.10.8. This enables implementing a curies.Converter that validates LUIDs with regular expressions, e.g., from the Bioregistry and also that removes redundant prefixes (i.e., bananas)
• CURIE parsing in curies.Converter.parse_curie was re-implemented to take into account the prefix map, rather than just splitting on a colon : in v0.10.7
• A new function curies.Converter.parse that can handle both CURIEs or URIs was added in v0.10.7

Feedback and bug reports: https://github.com/biopragmatics/curies/issues

Spotlight on LinkML

Bridging the Gap for Semantic Data Modeling

The Linked Data Modeling Language (LinkML) is increasingly utilized to support structured data modeling and enhance interoperability across ontologies and related data systems.

Ontologies provide a structured vocabulary for describing scientific concepts. However, researchers often collect data in formats like spreadsheets, where the meaning is only implied. Column headers, value types, and expected formats are rarely standardized, making it difficult and error-prone to integrate datasets across different laboratories or disciplines.

LinkML addresses this challenge by offering a schema framework that makes these underlying assumptions explicit and computable. It allows researchers to define classes, constrain values using ontologies such as ENVO or Uberon, and clearly document expectations about data structure, units, and formats, all in a way that is understandable for both humans and machines.

In practice, LinkML helps bridge the gap between domain knowledge (ontologies) and data structure (schemas), making the validation, integration, and reuse of datasets easier. LinkML not only supports ontologies; it also enhances their utility in real-world data workflows, helping to make scientific data FAIR (Findable, Accessible, Interoperable, and Reusable) and ready for reuse.

Learn more and get started:

• LinkML tutorial
• Using ontologies in LinkML schemas

Events and News

OBO at Biocuration 2025

The OBO Foundry community participated in the Biocuration 2025 conference at the Stowers Research Institute in Kansas City, Missouri.

Collaborative Biocuration and Training**

**A workshop on collaborative biocuration, co-led by Sabrina Toro (Monarch Initiative) and Nicole Vasilevsky (Critical Path Institute), presented approaches from the OBO Foundry to strengthen and support collaborative work and OBO Academy for providing accessible, version-controlled training resources. The session included case studies from PomBase, the Gene Ontology Consortium, and WormBase’s AI-supported annotation. Key topics were transparency, participation, and quality control in curation. Participants suggested developing a centralized training hub, broader certification options, and increased community exchange.

Slides are available here. Workshop summary is available here.

uPheno workshop: Enhancing the Unified Phenotype Ontology to Support Cross-Species Phenotype Interoperability

Led by Sue Bello (MGI) and Arwa Ibrahim (Monarch Initiative, EBI), the 4th uPheno workshop engaged participants from various ontologies and databases, including the plant community, the Rat Genome Database (RGD), the Mammalian Phenotype Ontology (MP), the Zebrafish Information Network (ZFIN), and the Database Center for Life Science (DBCLS), among others. The workshop focused on two main topics: 1) Improving the upper-level structure of the ontology and 2) Identifying integration and organization issues. Discussions also explored the current challenges in browsing the ontology, uPheno’s classification philosophy, reference ontology dependency, the utility of patternization for complex phenotypes, improving term labels and human-centric definitions, as well as leveraging AI to identify classification discrepancies. Future plans include working with plant ontology curators to integrate plant terms and developing collaborations with the RGD. Participants were encouraged to join the uPheno slack community, attend uPheno monthly calls, and create tickets in uPheno’s GitHub repository.

Slides are available here.

Ontology Automated Workflow for Ontology Community Curation

As part of her podium presentation about the Mondo disease ontology’s community approach to ontology maintenance, Sabrina Toro (Monarch Initiative) presented a workflow that allows the automated import of expertly curated community content directly into the ontology. This workflow relies on a simple spreadsheet maintained at the community source where the curation takes place. The content of this spreadsheet is automatically imported, quality-controlled, and added to the ontology with full provenance and attribution to the community source. This workflow is scalable and has been successfully implemented, for example, to maintain the Mondo rare disease subset.

Slides are available here

AI-Assisted Curation Tools

Presented by Harry Caufield, this podium presentation introduced the open-access tools OntoGPT and CurateGPT, which leverage large language models alongside trusted knowledge bases and literature sources. These tools enable biocurators to efficiently extract, annotate, and curate information from diverse scientific texts, linking extracted concepts directly to ontologies and supporting literature. By streamlining the curation process and improving data provenance, OntoGPT and CurateGPT help curators keep pace with the rapidly growing volume of scientific data.

Slides are available here

Overall, the OBO Foundry’s involvement at Biocuration 2025 focused on training, ontology integration, curation workflows, and the intersection of AI and biocuration.

OBO Academy: Seminar Series (ongoing)

• The OBO Academy: Seminar Series is run by members of the Monarch Initiative, but open to all. Please reach out in the OBO slack channel “#obo-academy” to be signed up.
• Schedule: https://oboacademy.github.io/obook/courses/monarch-obo-training/
• You can vote for and request training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace.
• OBO Foundry RSS feed at https://obofoundry.org/feed.xml
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are many ways in which you can contribute, including assisting with the production of this newsletter.

Happy New Year from the OBO Foundry Community!

In this edition, we highlight two of our dedicated community members and two OBO Foundry ontologies. You will also find updates on recent workshops, the latest tools to improve ontology development, and the progress of current projects.

As always, we encourage you to share your ideas, feedback, and suggestions with the OBO Foundry Operations Committee.

Highlights

OBO Dashboard updated

The OBO Foundry Dashboard tracks the progress of ontologies in meeting OBO Foundry principles, such as good metadata and interoperability. Ontologies that meet these standards are highlighted on the OBO Foundry homepage at https://obofoundry.org. We encourage all ontology developers to use the dashboard to check their ontologies and improve them. You can access the dashboard (last updated 2025-01-16) here: OBO Dashboard.

Ongoing Discussions

Editorial Working Group

The EWG focuses on refining the principles and guidelines that ensure consistency and quality across OBO ontologies.

• Principle 19, “Term Stability”: Revisions to Principle 19, focusing on how to handle obsolete terms, dominated the EWG’s recent discussions. The EWG decided to implement a check for the owl:deprecated property on classes containing “obsolete” or similar variations in their name or definition. They are also exploring methods, such as analyzing GitHub issue complaints, to assess term stability more comprehensively. The OBO community is welcome to comment on the proposed revisions to this principle.
• Principle 7, “Relations”: Discussions around Principle 7 aimed to provide clearer guidance on when relations should be added to the Relation Ontology (RO) or kept within a specific ontology. This is a recurring challenge, and the EWG proposed conditions focusing on a relation’s domain and range and its potential for broader use. A significant concern is preventing “relation striping,” where related terms end up defined across multiple ontologies. The proposed guidance is:
  1. If both the domain and range of a proposed relation belong to the same ontology, it is acceptable to keep the relation within that ontology. However, it should still have a parent term in RO if one exists.
  2. If only the domain of a relation belongs to the same ontology, the decision to include it in RO depends on whether the relation is invertible. Invertible relations, where the subject and object can be swapped, raise additional considerations.
  3. Relations with a domain outside the defining ontology should be added to RO.
  4. Relations considered generally usable (applicable in other ontologies) should also be added to RO.
  5. When in doubt, add the relation to RO. This principle encourages a preference for including relations in RO whenever possible. The EWG’s recommendations emphasize the importance of RO as the central repository for relations, promoting interoperability and consistency across OBO ontologies. However, several challenges and open questions remain:
     1. RO’s Comprehensiveness: RO might not yet be comprehensive enough to cover all possible relation types. What happens when a suitable RO parent term doesn’t exist for a relation that meets the criteria for remaining within a specific ontology?
     2. “Relation Striping”: This refers to the problem of related relations being defined across different ontologies, hindering clarity and findability. The EWG is considering how to prevent this, potentially by retroactively moving related relations into RO.
     3. COB’s Use of RO Relations: The relationship between COB and RO, specifically which relations COB should hold, is another ongoing discussion.
  6. The EWG is actively working on addressing these challenges and refining Principle 7 to provide clearer and more actionable guidance for ontology developers. This will improve the consistency and interoperability of relations across OBO ontologies.
• Naming Conventions: The EWG reported persistent issues with inconsistencies in naming conventions across ontologies. This includes variations in capitalization, the use of camel case and underscores, and the application of title case. Though each of these are considered violations of Principle 12 “Naming Conventions”, there are numerous cases where such are warranted, such as capitalized genus names in taxonomies. Acknowledging the need for exceptions in certain cases, the EWG is working towards establishing mechanisms to distinguish between warranted exceptions and true violations.

Discussions are ongoing, with the committee actively seeking feedback (which you can provide by commenting on Principles 7 and 12) and working towards revised versions of these principles.

Ontologies

New ontologies currently under review

• PRIDE (Proteomics Identification Ontology): The PRIDE (Proteomics Identification) Ontology provides a structured framework for describing and sharing proteomics data from mass spectrometry experiments, organizing information in the PRoteomics IDEntifications Database. The ontology includes terms for protein identifications, peptide sequences, experimental conditions, and modifications, enabling researchers to consistently annotate their data across different studies. Join the discussion.
• Membrane Ontology (MEMON): The Membrane Ontology creates a structured vocabulary for annotating biological data about cell membranes and their experimental and computational models, allowing detailed membrane descriptions and connections between datasets. The terms cover different biological membrane models used in research, along with their component descriptions, and will expand to link models with the types of biological membranes they approximate. Join the discussion.

Spotlight on well-established OBO ontologies

In this issue, we continue our ontology spotlight series, highlighting two ontologies from the OBO Foundry family, the FlyBase Controlled Vocabulary (FBcv) and the Mammalian Phenotype Ontology (MP).

• The Mammalian Phenotype Ontology (MP) provides a structured vocabulary for curation and retrieval of mammalian phenotypes. Originally developed for use by Mouse Genome Informatics (MGI) and Rat Genome Database (RGD) over 24 years ago, the MP currently consists of more than 14,200 pre-composed phenotype terms organized across 28 broad categories. These terms have been used to curate phenotypes for over 74,800 mouse models in MGI. New releases are published on a monthly basis and are available from the MGI download page or the MP GitHub repository. New terms are added based on user requests and as part of systematic reviews and revisions. Recent updates have focused on expanding coverage for models of pediatric diseases that are part of the Gabriella Miller Kids First initiative (including idiopathic scoliosis, cleft palate, and congenital heart disease), reproductive system terms with a focus on infertility models, and COVID-19 models. During revisions we work on enhancing the alignment between the MP and the Human Phenotype Ontology (HPO) both by improving consistency of logical definitions across the ontologies and by manual mapping of MP and HPO terms using the SSSOM format. The mapping files are available in the Mouse-Human Ontology Mapping Initiative GitHub repository. The MP has become an integral part in disease model identification and disease gene prediction and the ongoing work will enhance the utility of the MP for researchers, clinicians, and curators. Questions and suggestions should be directed to the MP GitHub issue tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues).
• The FlyBase Controlled Vocabulary (FBcv) has existed as an ontology since at least 2007 and was intended to provide controlled terms for describing Drosophila genetic entities and associated data. Alleles in FlyBase have detailed, standardised annotations, with information about encoded tools (such as GFP) and types of functionality (e.g. conditional loss of function) curated using FBcv. Phenotype curation uses the Drosophila Phenotype Ontology, which is incorporated into FBcv (as well as being available as a standalone file) plus qualifier terms (such as ‘somatic clone’), which are also found in FBcv. There are also terms to describe publications (e.g. ‘paper’) and datasets, including methodologies and sample attributes. FBcv has been on GitHub since 2015 and using the Ontology Development Kit since 2019. Most term additions over the past year have been new types of genetic tools, reflecting the diverse manipulations possible in this model organism.

Members and Volunteers

The OBO Foundry is honored to highlight two valued community members.

Nicole Vasilevsky

Nicole Vasilevsky is the Associate Director of Data Science at the Critical Path Institute (C-Path), which is based in Tucson, AZ (USA) but she works remotely with her cats from the coffee-loving city of Portland, OR (USA). Her journey into the world of ontology curation began in the lab of Melissa Haendel at Oregon Health & Science University, where she was initiated into ontology development through her work on the eagle-i Network. As one of the original members of the Monarch Initiative, she helped develop tools that utilize ontologies for disease diagnostics. She has contributed to various OBO ontologies, including the Human Phenotype Ontology (HPO) and Mondo Disease Ontology, where she served as the original curator and lead and remains an active contributor. After sharing fears about “breaking” ontologies with colleagues at the International Conference on Biomedical Ontology (ICBO), Nicole began contributing to the OBO tutorials at ICBO to train ontology developers. This experience led her to consult at C-Path, collaborating with colleagues to train team members in ontology development and laying the foundation for the OBO Academy. Since joining Ramona Walls’ team at C-Path in January 2023, she is currently focused on standardizing rare disease data through the Rare Disease Cures Accelerator - Data and Analytics Platform (RDCA-DAP). Nicole serves on the OBO Foundry Operations Committee and values the mentorship and collaborations she’s fostered in the community and hopes our work will enhance our understanding and treatment of rare diseases.

Chris Mungall

Dr. Chris Mungall is a Senior Scientist in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory, where he heads the Biosystems Data Science department. Chris’s research involves the curation and integration of biological research data to elucidate biological mechanisms underpinning the health of humans and of the planet. He is a PI on both the Gene Ontology (GO) project and the Monarch Initiative.

Chris has a background in knowledge representation, and was one of the original founding members of the OBO Foundry. He has led or made major contributions to multiple ontologies such as the GO, Uberon, ENVO, Mondo, and RO. He has helped pioneer ontology-related standards such as LinkML, the Knowledge Graph Change Language (KGCL), and SSSOM, and his team has helped build an ecosystem of tools around OBO, including the Ontology Access Kit (OAK), and LLM-based tools including OntoGPT.

In 2017, Chris was the first person to be awarded the Exceptional Contributions to Biocuration Award by the International Society for Biocuration.

Spotlight on Research in the OBO community

A change language for ontologies and knowledge graphs

Ontologies and knowledge graphs evolve constantly as scientific knowledge grows. A new framework, KGCL (Knowledge Graph Change Language), offers a standardized way to track and implement these changes. KGCL uses clear commands like “rename X to Y” that both humans and computers can understand.

The system comes with practical tools: Ontobot processes changes through GitHub automatically, while a new BioPortal widget lets users suggest updates through a simple interface. These tools are already being used by Mondo, GO, ENVO, and Uberon. KGCL helps ontology teams work more efficiently while making it easier for the broader scientific community to contribute.

The development of KGCL was driven by community needs, in particular a 2023 workshop attended by many OBO ontology developers and curators. As ontologies continue to grow in importance for biological research, KGCL offers a timely solution for keeping these vital resources up to date.

Figure from Hegde H, Vendetti J, Goutte-Gattat D, Caufield JH, Graybeal JB, Harris NL, Karam N, Kindermann C, Matentzoglu N, Overton JA, Musen MA, Mungall CJ. A change language for ontologies and knowledge graphs. 2025 Jan 22 https://doi.org/10.1093/database/baae133.

Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Many of the ontologies in OBO are large, with tens of thousands of classes, many of these classes interlinked via OWL axioms. Some of these ontologies are too large to use with most OWL reasoners. A major game changer for the OBO world was the release of the ELK reasoner, which was fast enough to reason over large ontologies like GO, CL, and Uberon. One reason ELK is so much faster than other reasoners is that it operates over a restricted subset or profile of the OWL language (formally called EL++). However, this tradeoff means that ELK can’t operate over all axiom types, including certain kinds of rule axioms found in the Relation Ontology.

Whelk is a new reasoner that allows for reasoning over both OWL EL, as well as the OWL RL profile, giving ontology editors additional expressivity when reasoning with instance graphs and rules. Developed in Scala with immutable functional data structures, Whelk excels in handling high-throughput queries and dynamic reasoning tasks, outperforming traditional reasoners like ELK in specific scenarios.

The reasoner supports complex class expressions and SWRL rules, enabling rapid instance reasoning, parallel query processing, and incremental updates without affecting prior ontology states. Applications include relation graph materialization, biomedical ontology reasoning, and enhanced query performance for large ontologies such as Uberon and the NCI Thesaurus.

Whelk demonstrates its utility in real-world scenarios, such as the Ubergraph knowledge graph pipeline, executing millions of DL queries efficiently, allowing for precomputation of different valid paths through the ontology.

Whelk is available as a Protege plugin, and can be easily dropped into existing ODK pipelines, or used in combination with ROBOT. Whelk has already been adopted as the default reasoner by the Cell Ontology (CL).

Figure from James P. Balhoff (University of North Carolina, Chapel Hill) and Christopher J. Mungall (Lawrence Berkeley National Laboratory). Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. 2024 Dec 18; https://doi.org/10.4230/TGDK.2.2.7

A general strategy for generating expert-guided, simplified views of ontologies

This preprint introduces a strategy for creating expert-guided, simplified views of complex biomedical ontologies to support FAIR data practices. Caron et al. (2024) address challenges faced by researchers using detailed ontologies like Uberon and Cell Ontology (CL) by developing tools to validate user hierarchies and generate tailored ontology views.

Applied in projects like HuBMAP and Human Developmental Cell Atlas (HDCA) these workflows simplify ontology use while ensuring accuracy. Automated validation pipelines and visualization tools enhance alignment between user needs and ontology structures, fostering collaboration between researchers and curators.

The tools, available at https://github.com/hubmapconsortium, offer a practical approach to integrating ontology-driven data annotation and analysis.

Figure from Anita R. Caron, Aleix Puig-Barbe, Ellen M. Quardokus, James P. Balhoff, Jasmine Belfiore, Nana-Jane Chipampe, Josef Hardi, Bruce W. Herr II, Huseyin Kir, Paola Roncaglia, Mark A. Musen, James A. McLaughlin, Katy Börner, and David Osumi-Sutherland. A General Strategy for Generating Expert-Guided, Simplified Views of Ontologies. 2024 Dec 18; https://doi.org/10.1101/2024.12.13.628309)

Spotlight on OBO Principles

Principle 6 of the OBO Foundry emphasizes the importance of textual definitions for ontology terms. A textual definition is a clear, human-readable explanation of what a term represents, helping researchers understand its meaning and use. These definitions should be unique, written in English, and ideally follow a structure like “a B that Cs,” where B is the broader category and C specifies the unique characteristics. Textual definitions should align with logical definitions (used by machines) to avoid confusion in classification or annotation.

The principle allows flexibility through alternative approaches - terms that resist strict definition can use elucidations, and definitions can be generated programmatically using Dead Simple Ontology Design Patterns (DOSDPs). For optimal clarity, usage examples and editorial notes should be kept separate from the core definition. Though instances like organizations or locations may have definitions, they aren’t required for these cases.

We recommend that anyone who writes ontology definitions reads this excellent blog post by Chris Mungall from 2019: https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/.

While the OBO Dashboard only reports a warning when classes are not defined (for practical reasons), we want to remind the community that definitions are important to enable both humans and AI agents to understand and recognise the concept defined. Labels alone are often ambiguous. You are doing your human users and future AI assistants a big favour if you take writing human-readable definitions seriously.

Spotlight on Tools: Recent updates

Babelon for ontology translations

Babelon for ontology translations. The Babelon format is a simple spreadsheet-based format to curate and integrate ontology translations. It has been implemented by various widely used ontologies such as HPO, MP and Mondo. It can be used by ODK-managed ontology systems to publish “international editions” of an ontology. Those international editions can be leveraged by ontology browsers such as OLS to display the ontology in various languages; see below. The Babelon toolkit supports operations such as simple, AI-assisted translation of the entire ontology. Some example Babelon files can be found here. More information about Babelon workflows can be found in this presentation.

ROBOT-Template Helper

The ROBOT-Template Helper GPT is a tool designed by Chris Mungall to assist researchers in creating ontology templates for use with ROBOT, a set of tools for building ontologies that is commonly employed in the OBO (Open Biological and Biomedical Ontologies) community. It helps users generate structured CSV files that define ontology classes, relationships, and metadata in a format compatible with ROBOT’s template system. The tool supports adding annotations, logical axioms, and mappings to ontology terms, ensuring alignment with best practices for ontology development. By simplifying template creation, it enables users to efficiently build and manage domain-specific ontologies. For more information please check AI Guided Ontology Curation Workflows and the ROBOT Template GPT helper

Spotlight on Newly Approved Grants

Developing an Ontology for Dental Care-Related Fear and Anxiety (ODFA): Toward an Understanding of Problems in Dental Care Utilization

Principal Investigators: Bill Duncan, Daniel McNeil

NIH Reporter: https://reporter.nih.gov/search/LGKYr0JMlkauBjcllqzKaw/project-details/10939840

Dental care-related fear, anxiety, and/or phobia (hereafter, DFA) traditionally refers to the emotional, behavioral, and/or physical responses that may occur when thinking about or engaging in dental care. There is ample evidence in the scientific literature that DFA is associated with greater prevalence of oral conditions and diseases, including dental caries, tooth loss, and periodontal disease, leads to avoidance of both preventive and restorative dental care, and impairs oral health-related quality of life.

Despite the impact of DFA on oral health, the scientific literature is replete with terminology that refers only to dental fear or only to dental anxiety, yet in the broader psychological literature, fear and anxiety are known to be separate constructs with unique manifestations. This lack of consistency and interoperability between the medical and dental care communities in defining and classifying such phenomena has contributed to the current stalemate in scientific progress as it relates to understanding the etiology and implications of such phenomena in the dental care context. Without a consensus on the definition, types, scope, and etiology of DFA, the associated individual, clinical, and population impacts, and viable strategies for intervening to mitigate or manage such impacts the impact of DFA cannot be adequately studied. To address these terminological shortcomings, we have created the Ontology of Dental care-related Fear, and Anxiety, and/or Phobia (ODFA). By more precisely representing the types of fear and/or anxiety experienced by individuals, the ODFA’s concepts and relations facilitate the development of tools and resources capable of enhancing our understanding of the individual, clinical, and population impacts of dental care-related fear and anxiety. When applied to study data, the ODFA enables the integration and interoperability of data from multiple studies, which, in turn, provides a means to perform rigorous analysis on larger datasets in order to gain an in-depth understanding of the phenomenon and treatments for DFA.

Spotlight on Tools: Ontology Browsers

Popular ontology browsers include the Ontology Lookup Service (OLS), Ontobee, and BioPortal. We spotlight OntoBee in this issue.

Ontobee

Ontobee is the default resolver for many OBO ontologies and an essential tool for exploring them. Every ontology page on the OBO website includes a link to view that ontology in Ontobee. A major strength of Ontobee is its ability to display complex OWL axioms for ontology terms, which can also be retrieved programmatically. This makes it a valuable resource for ontology term dereferencing, linkage, and integration.

Ontobee is a collaborative project involving different parties. The source code of the Ontobee software is developed and maintained by the He Group. Ontobee performs weekly updates, automatically retrieving ontology sources and metadata from the OBO Foundry. Ontobee is part of a suite of tools (including Onto-Animals) that offer complementary features to support ontology exploration and usage, which will be highlighted in future newsletters.

For Ontobee software questions and feature requests, contact the Ontobee-discuss group (ontobee-discuss@googlegroups.com) or submit issues on GitHub (https://github.com/ontoden/ontobee/issues). Principal Contact: Dr. Yongqun “Oliver” He, University of Michigan Medical School, Email: yongqunhe@gmail.com

For further details, see:

Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He, Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D347–D352, https://doi.org/10.1093/nar/gkw918.

Events and News

• ChEBI workshop. The ChEBI workshop was held on 19th November 2024 at the European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom. ChEBI (Chemical Entities of Biological Interest) is a freely available database and ontology focused on small molecular entities. It provides a curated repository of chemical information that supports the life sciences research community.

  The 1-day workshop was conducted as a hybrid event, with 24 in-person and 12 remote participants. Its primary aim was to bring together stakeholders from major bioinformatics resources that rely on ChEBI, provide updates on ChEBI’s redevelopment, receive feedback, and solicit further input. Representatives from various bioinformatics resources, including GO, UniProt, Rhea, MetaboLights, OLS, EuropePMC, PubChem, Reactome, IEDB, GlyGen, and LIPID MAPS, were present. Eloy Felix provided an overview of ChEBI’s history, technical landscape, and future goals. Muhammad Arsalan presented updates on ChEBI’s new web interface, advanced search functionality, and manual/automatic cross-references. Adnan Malik discussed the new submissions portal, while Carlos Moreno explained ChEBI’s ontology generation process and download formats. Juan Mosquera covered the new REST web services and the implementation of some new endpoints. The meeting concluded with Andrew Leach initiating discussions about ChEBI’s operating model and future funding. Additionally, five representatives from different resources gave talks introducing their resources, explaining how ChEBI is used within them, and suggesting potential improvements. Ozgur Yurekten presented MetaboLights, Kristian Axelsen presented Rhea, Peter D’Eustachio presented Reactome, Chris Mungall presented GO’s needs for a simpler version of CHEBI, and Randi Vita presented IEDB. The day was productive, marked by active discussions and constructive feedback. Many participants appreciated the idea of further developing ChEBI through community efforts, akin to the GO consortium model—opening up curation of the ontology part of CHEBI to a set of trusted partners. Some of the workshop slides can be found here: https://drive.google.com/drive/folders/1XMlzZFXXm7styUhzOBgpWchiwLutQj4f.

• The 18th Annual International Biocuration Conference:

  The 18th Annual International Biocuration Conference will take place from April 5 to 9, 2025, in Kansas City, Missouri, hosted by the Stowers Institute for Medical Research. This conference serves as a platform for professionals involved in the curation, development, and utilization of clinical and life sciences data to share their work and collaborate. Keynote speakers include experts from institutions such as Ohio State University, the University of Minnesota, the Allen Institute, the University of Arizona, EMBL-European Bioinformatics Institute, and the University of Southern California. Registration is open until February 28, 2025, or until capacity is reached. The event is organized in collaboration with the International Society for Biocuration (ISB).

• OBO Academy: Monarch Seminar Series (ongoing)
• Schedule: https://oboacademy.github.io/obook/courses/monarch-obo-training/
• You can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace.
• OBO Foundry RSS feed at https://obofoundry.org/feed.xml
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are many ways in which you can contribute, including assisting with the production of this newsletter.

Welcome to the 6th issue of the OBO Foundry Newsletter! As always, we’re excited to share the latest developments and achievements in the bio-ontology community.

This edition continues our tradition of spotlighting contributors and ontologies. We’re pleased to introduce two of our dedicated community members, as well as two ontologies that exemplify the principles and standards of the OBO Foundry.

We will report on the progress of ongoing initiatives, including updates on ontology reviews, Principal standardization efforts, and new tools that are enhancing our collective work.

This issue also features a recap of recent events and workshops that have fostered collaboration and knowledge-sharing within our community.

As always, we invite you to share your thoughts, ideas, and suggestions with the OBO Operations Committee. Your input is invaluable in shaping the future of the OBO Foundry and advancing our shared mission of creating interoperable, high-quality ontologies for biomedical research.

Best regards, The OBO Foundry Operations Committee.

Highlights

New Dashboard release

Our dashboard reflects the ongoing commitment of our community to harmonize metadata and increase interoperability across ontologies. We continue to invite the community to participate in the harmonization efforts, and get their ontologies to pass the dashboard. Ontologies that pass are highlighted on https://obofoundry.org/. The latest version of the dashboard can be accessed here: https://dashboard.obofoundry.org/dashboard/index.html.

Ongoing Discussions

Principle 19 Development: Shaping Guidelines for Term Stability and Deprecation

There is an ongoing discussion about the development and refinement of Principle 19. The discussion covers circumstances that require the obsoletion of terms and the stability of their meanings. The draft of Principle 19 is currently in progress and focuses on term stability and deprecation.

• Key points include:
  • Defining circumstances for term deprecation
  • Distinguishing between mandatory and recommended practices
  • Exploring alternatives to the “obsolete class” method
    • The committee discussed that all alternative identifiers (alt IDs) should be explicitly marked as obsolete. Furthermore, the OFOC decided that prepending “obsolete” to the label of an obsolete term is mandatory while prepending “obsolete” to the definition of an obsolete term is recommended but not mandatory.
  • Documenting reasons for term obsoletion
  • Ensuring timely communication about deprecated terms
  • Automated compliance checks
• The committee is considering:
  • Using “must,” “should,” or “may” to indicate obligation levels
  • Implementing automated checks for adherence to the principle
  • Integrating the principle into ROBOT reports

Discussions are ongoing, with the committee actively seeking feedback (which you can provide by commenting on the issue) and working towards a revised draft.

Ontologies

New ontologies currently under review

• Exercise Medicine Ontology (EXMO) is an ontology focused on exercise medicine. It is based on the Basic Formal Ontology (BFO), and includes terms related to physical activity, health status, and exercise prescriptions for various populations, including healthy individuals, those with chronic conditions, and people with disabilities. Developed to support personalized exercise prescriptions, EXMO bridges standardized guidelines with individualized approaches. It draws from guidelines, databases, and scientific literature and has been validated through expert evaluation and reasoners like ELK and JFact. Currently under review, EXMO aims to become a standard for personalized exercise prescriptions and a tool for databases and recommendation systems. Join the discussion.
• Biomarker Ontology (BMONT) is a comprehensive knowledge representation system that encompasses various medical and biological aspects. Developed in accordance with Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) principles, BMONT builds upon a decade-old biomarker terminology created by Fraunhofer SCAI. It incorporates entities and definitions from this legacy system, as well as related terms gathered from scientific publications and books across diverse disease fields. The ontology aims to enhance biomarker identification tasks and serve as a supportive, integratable tool for advanced AI techniques such as Machine Learning (ML) and Large Learning Models (LLM). BMONT is under review, with contributors actively addressing feedback and making updates to improve its quality and alignment with OBO Foundry standards. Join the discussion.
• Physiologically based pharmacokinetic modelling ontology (PBPK) is a framework for representing the complex pharmacokinetic processes in living organisms. It includes classes like physiological parameters, PBPK types, biological compartments, and mathematical models, aiding in understanding drug behavior. This ontology provides a structured vocabulary for researchers, clinicians, and drug developers, promoting communication, data integration, and collaboration in pharmacokinetics and related life sciences. PBPK is currently under review - join the discussion.

Spotlight on well-established OBO ontologies

In this issue, we continue our ontology spotlight series, highlighting two ontologies from the OBO Foundry family, the Medical Action Ontology (MAxO) and the Drug Ontology (DrOn).

• The Medical Action Ontology (MAxO) aims to provide a standardized framework for describing and organizing medical actions, particularly in the context of phenotypic annotations. This ontology plays a role in harmonizing the diverse terms used in clinical settings, making it easier for researchers and healthcare professionals to communicate effectively. A recent development in MAxO involves the integration of treatment annotations to phenotypes into the Human Phenotype Ontology (HPO) website (example, click on “Medical Action”). This update enhances the utility of HPO for researchers, allowing them to explore comprehensive annotations in one place, which improves disease diagnosis and phenotype-based research.
• The Drug Ontology (DrOn) is a structured, formal representation of drug-related knowledge that organizes information about pharmaceuticals, their properties, ingredients, and relationships in a standardized format. It provides a common vocabulary and hierarchical classification system for drugs, containing aspects such as chemical structure, therapeutic uses, and mechanisms of action. Drug ontologies play a crucial role in various fields, including pharmacology, clinical research, and healthcare informatics, by facilitating data integration, enhancing interoperability between different systems, and supporting advanced applications like drug discovery, adverse event prediction, and personalized medicine. DrOn aims to provide a comprehensive classification of drug products and their ingredients, reusing the Chemical Entities of Biological Interest (ChEBI) ontology for compounds that are drug ingredients. It reuses other OBO ontologies as needed, including the Protein Ontology and the Information Artifact Ontology. Since its creation, DrOn has been semi-automatically built from the RxNorm drug terminology provided by the National Library of Medicine. Because RxNorm is not available in OWL or OBO format, DrOn represents the only principled OWL and OBO format version of key RxNorm content useful for automatically classifying drugs by their various properties. This process of automatically creating large segments of DrOn from RxNorm recently underwent a major overhaul in collaboration with James Overton. The entire DrOn build from monthly RxNorm releases is now encapsulated in DrOn’s Ontology Development Kit (ODK) processes in Docker, enabling DrOn curators with less technical expertise to manage the entire monthly build and release process

Members and Volunteers

The OBO Foundry is honored to highlight two valued community members.

Bill Hogan

William “Bill” Hogan, MD, MS is currently Professor and Director of the Data Science Institute at the Medical College of Wisconsin, where he holds the Mary T. and Ted D. Kellner Chair of Data Science. He has over 20 years of experience in the development, maintenance, and application of biomedical data standards, especially ontologies. He created the Drug Ontology (DrOn) to facilitate comparative effectiveness research on medications. He also leads the development of the Ontology for Modeling and Representation of Social Entities (OMRSE), which represents healthcare organizations, healthcare providers, healthcare roles, as well as numerous social determinants of health including education, language and literacy, socio-economic status, social identities and categories, and intimate partner violence. He previously held R01 funding from NIGMS to create data standards for epidemic simulators and disease transmission models, which includes the Apollo-SV ontology. Apollo-SV represents numerous aspects of the infectious disease epidemiology domain.

Sarah Gehrke

###

Sarah (she/they) is a Research Program Project Manager with the Translational and Integrative Sciences Lab (TISLab) at the University of North Carolina at Chapel Hill’s Department of Genetics. With a background as an analytical chemist, Sarah brings diverse experience from industry labs which focused on coal and natural gas remediation and biomass conversion technologies. She also participated in metabolomics mass spectrometry research at the University of Colorado Anschutz Medical Campus (CU-AMC) and served as Finance Manager for the Structural Biology and Biochemistry Cores at the CU-AMC School of Medicine.

In 2022, Sarah transitioned to her current role as Project Manager for the TISLab. Sarah manages the Monarch Initiative, providing key support for the Mondo Disease Ontology, the Monarch Knowledge Graph, and Human Phenotype Ontology. She is a driving force behind OBO Academy, managing the ongoing Seminar series, curating training materials and recruiting speakers. Sarah is passionate about connecting people to drive fundamental, positive changes that enhance community wellness.

Spotlight on Research in the OBO community

A Change Language for Ontologies and Knowledge Graphs

The research outlines the Knowledge Graph Change Language (KGCL), a new standard data model for describing changes to knowledge graphs (KGs) and ontologies. KGCL aims to standardize and simplify the process of managing changes in these complex data structures, making it easier for stakeholders to understand and contribute to the development of ontologies and KGs. The preprint details the structure of KGCL, its controlled natural language (CNL), and various tools developed to support the use of KGCL, such as the Ontobot automated agent and a BioPortal widget for requesting changes to ontologies. The paper also discusses future directions for KGCL, including its use in AI applications and integration with other frameworks.

(Figure from Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J Harry Caufield, John B Graybeal, Nomi L Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A Overton, Mark A Musen, Christopher J Mungall. A Change Language for Ontologies and Knowledge Graphs. 2024 Sep 20; https://arxiv.org/abs/2409.13906)

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

This preprint describes the development of the Unified Phenotype Ontology (uPheno), a framework designed to integrate and standardize phenotype data across multiple species. uPheno addresses the challenge of integrating phenotype data from different sources by providing a consistent and logical framework for describing phenotypes. It utilizes a library of design patterns to define phenotype terms, enabling the development of a hierarchical vocabulary that groups species-specific phenotype terms under species-neutral categories. uPheno also includes mappings between species-specific ontologies, facilitating cross-species comparisons and enabling researchers to identify genes with similar phenotypic effects across different organisms. The paper highlights the potential applications of uPheno in various areas of biological research, including clinical diagnostics, variant prioritization, and disease modeling.

(Figure from Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M. Alghamdi, Anna V. Anagnostopoulos, James P. Balhoff, Meghan A. Balk, Yvonne M. Bradford, Yasemin Bridges, Tiffany J. Callahan, Harry Caufield, Alayne Cuzick, Leigh C Carmody, Anita R. Caron, Vinicius de Souza, Stacia R. Engel, Petra Fey, Malcolm Fisher, Sarah Gehrke, Christian Grove, Peter Hansen, Nomi L. Harris, Midori A. Harris, Laura Harris, Arwa Ibrahim, Julius O.B. Jacobsen, Sebastian Köhler, Julie A. McMurry, Violeta Munoz-Fuentes, Monica C. Munoz-Torres, Helen Parkinson, Zoë M Pendlington, Clare Pilgrim, Sofia MC Robb, Peter N. Robinson, James Seager, Erik Segerdell, Damian Smedley, Elliot Sollis, Sabrina Toro, Nicole Vasilevsky, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall, James A. McLaughlin, and David Osumi-Sutherland. The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics. 2024 Sep 20. https://www.biorxiv.org/content/10.1101/2024.09.18.613276v1

Spotlight on OBO Principles

In this issue, we continue with Principle 5 of the OBO Foundry’s series of principles.

OBO Foundry Principle 5: Scope

OBO Principle 5 addresses the importance of a clearly defined scope for ontologies. It emphasizes that each ontology should have a well-specified domain or subject matter it intends to cover, and its content should adhere strictly to that scope. This principle aims to avoid overlaps between ontologies, facilitate user searches, and enable quick selection of relevant ontologies while still allowing for the creation of new terms through cross-products. The scope of an ontology should ideally be narrow, with out-of-scope terms imported from appropriate existing ontologies when possible. If an immediate need arises for out-of-scope terms, they should be placed in a separate, shareable module. The ontology’s domain should be clearly stated in a brief, jargon-free manner, and its content should remain within these defined boundaries. This principle also encourages consideration of generic and mid/upper level terms for potential inclusion in the Core Ontology for Biology and Biomedicine (COB), ensuring that the ontology serves both its specific purpose and broader community needs.

Spotlight on Tools: Recent updates

Simple Standard for Sharing Ontological Mappings (SSSOM) v. 1.0.

While the goal of the OBO community is to develop a set of interoperable ontologies covering the biomedical domain, many vocabularies, terminologies and ontologies are used globally which need to be linked to OBO ontologies. The SSSOM community standard was developed to provide an easy way to specify and exchange such mappings with rich provenance. After more than 4 years of work, with 79 contributors writing more than 1200 comments the first stable release is finally out:

https://github.com/mapping-commons/sssom/releases/tag/v1.0.0. A short post about the release was published on LinkedIn by the Monarch Initiative.

Spotlight on Tools: Ontology Browsers

Here and in upcoming issues of this newsletter, we would like to highlight some key ontology browsers: the Ontology Lookup Service (OLS), Ontobee, and BioPortal. We spotlight BioPortal in this issue; watch for spotlights on Ontobee and OLS in future issues.

BioPortal

BioPortal is a web-based repository and collaborative platform for biomedical ontologies and terminologies developed by the National Center for Biomedical Ontology (NCBO). It is a centralized resource for accessing, browsing, and integrating standardized biomedical vocabularies and ontologies. The platform utilizes semantic web technologies to enhance interoperability and data integration across biomedical domains. BioPortal’s collection contains numerous ontologies covering fields such as anatomy, phenotypes, experimental conditions, and molecular functions. BioPortal also offers ontology visualization tools, mapping services, and programmatic access via web services, facilitating knowledge management and semantic annotation of biomedical data.

Events

• COB Workshop. Purpose: To advance the development of COB.

  The 2024 COB Workshop was held September 23–24 at The La Jolla Institute for Immunology in San Diego, CA.

  The workshop included 10 in-person and 8 remote participants. Both days were quite productive with lively discussions and consensus building. Decisions were made and documented as described below and tabled discussions were tracked for future work, with the goal of focusing discussion on topics that were most likely to result in actionable decisions. The mechanism was to go through terms included in the present COB release, and review each term to decide whether it should be part of COB base (with COB IDs, label and definitions that would replace existing terms), COB full (imported terms from existing ontologies that can be used as is, which are needed in the axiomatization of COB), and COB root (imported terms from existing ontologies that are not needed to define COB, but that are included to illustrate how existing OBO ontologies will be able to connect). Much of the discussion on Day 1 focused on macromolecules and cells, working through many of the significant material entities for the remainder of the day. Day 2 started with a focus on human-made devices and material processing terms, with the goal of using COB to align existing terms from OBI and FOODON. Specimens and their collection from anatomical entities were also briefly discussed. Finally, a proposal on how to consistently define stages, phases, and cycles was discussed; different groups have modeled them as material entities, characteristics, biological processes, or time intervals/processes. The proposal was to consistently capture these as subclasses of processes in COB and to characteristics such as PATO:duration to link these to time intervals. Overall, more than half of the COB terms were discussed and a (preliminary) classification was made. Many participants requested future focused virtual meetings to continue COB development using the same strategies, to tackle the remaining terms, and get input from a broader community.

  If you are interested in this work, please watch and contribute to the COB repository: https://github.com/OBOFoundry/COB, and stay tuned for a more detailed workshop summary, which will be available in Issue 7 of the newsletter!

• OBO Academy: Monarch Seminar Series (ongoing)
• Schedule: https://oboacademy.github.io/obook/courses/monarch-obo-training/
• You can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Past Events

Fostering Open Science Collaborative Workflows: Insights from the ICBO OBO Tutorial

By Nicole Vasilevsky and Sabrina Toro

The OBO Foundry Training at ICBO 2024 took a close look at the social workflows surrounding ontology development. Topics such as GitHub, Pull Requests, review and principles of good collaborative work were discussed in depth. A recording is available at the above link.

Every year at the International Conference on Biological and Biomedical Ontology (ICBO), members of the Open Biological and Biomedical Ontology (OBO) Foundry host an OBO Tutorial to share insights into our latest work on ontology development, share best practices, and exchange knowledge. These OBO tutorials have become part of the OBO Academy (https://oboacademy.github.io/obook/), with special attention to training newcomers to semantic engineering. This year’s virtual tutorial was organized by Nico Matenzoglu (Semanticly) and Nicole Vasilevsky (Critical Path Institute) and focused on “Fostering Open Science Collaborative Workflows”. More details, including a recording of the session, are available here: https://oboacademy.github.io/obook/courses/icbo2024/

We discussed the importance of collaboration in the development of OBO ontologies. James Overton introduced the OBO Foundry, Sabrina Toro discussed Git and GitHub, Nico Matentzoglu discussed best practices in collaborative workflows and Nicole Vasilevsky shared best practices in creating GitHub tickets, submitting pull requests (PRs), and reviewing PRs in ontology repositories.

Thanks to a generous microgrant from the International Society for Biocuration we were able to offer small prizes for participating in a training quiz integrated into the tutorial. We awarded prizes to the top 5 participants with the most correct answers and 5 prizes to participants who answered the most questions, regardless of their answers. The winners were (in alphabetical order): Hannah Blau, Spencer Bliven, Yvonne Bradford, Lauren Chan, John Graybeal, Harshad Hegde, Bryan Laraway, Katie Mullen, Sumir Pandit, and Umasri Sankarlal.

Following the session, we hosted the OBO Community Challenge, which was open to all. The challenge provided an opportunity to apply the lessons learned from the OBO tutorial at ICBO. Participants were asked to choose one or several OBO ontology projects in which they were not involved yet, and complete a set of tasks (including opening an issue and creating a pull request) demonstrating the basic principles of collaborative workflows introduced at the tutorial. Ontology contributions were reviewed for the quality of the commit messages, and issue and pull request descriptions. We are very grateful to everyone who participated. The prizer was awarded to Paula Duek Roggli and Katie Mullen.

This was our inaugural opportunity to award prizes to participants in the OBO tutorial and OBO challenge. We believe these prizes enhanced engagement and boosted participation within the community. We extend our heartfelt gratitude to the ISB and the OBO Foundry community for their support, and to the ISB for backing the microgrant initiative. We also encourage everyone to get involved with and support the ISB—you might be the next recipient of a similar microgrant.

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace.
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are many ways in which you can contribute, including assisting with the production of this newsletter.

Welcome to the 5th issue of the OBO Foundry Newsletter. In this edition, we highlight the progress and achievements of our ontology developers and researchers in driving innovation and collaboration in biomedical research.

The biggest news in this issue is the change to the OBO Foundry homepage to highlight ontologies that meet OBO Foundry principles (as determined by the OBO Dashboard). We also discuss the ongoing efforts to enhance metadata standards, the decision about new ontology submissions, and the various initiatives undertaken by the OBO Operations Committee to streamline processes and foster active participation.

This issue also highlights well-established ontologies, dedicated members and volunteers, advanced research, foundational principles, and essential tools. We provide updates on past events and announce the numerous upcoming opportunities for learning and collaboration, which promise to shape the future of biomedical research.

Best regards, The OBO Foundry Operations Committee.

Highlights

OBO Foundry Home Page now highlights ontologies that meet OBO Foundry principles

The OBO Foundry front page now visually promotes ontologies that pass the basic metadata requirements implemented by the OBO Dashboard (described below). Ontologies with no dashboard errors are listed first in their section; those with errors are at the end, with gray-shaded backgrounds (as shown in the screenshot above). We hope that ontology developers will take this as an incentive to update their metadata records! Get help in the #dashboard channel in the OBO-community Slack workspace. The team is ready to support you!

OBO Foundry dashboard analysis

The OBO Foundry Dashboard is a tool that automatically checks ontologies in the OBO Foundry for adherence to the OBO Foundry principles). It provides:

• A report on each ontology’s compliance with the 20 principles (green means an ontology meets the principle; pink means it does not; yellow means there was a warning). An ontology is considered to “pass” the dashboard if it has no errors.
• Overall statistics about the ontologies in the OBO Foundry, including the breakdown of how many ontologies currently pass the checks broken down by OBO principle (see Figure below).

The dashboard aims to inform both users and developers, allowing users to quickly assess an ontology’s quality and helping developers of the ontologies identify areas for improvement. The OBO Foundry announced last year that passing the dashboard would become mandatory for all ontologies on January 1, 2024, and that non-compliant ontologies would be listed at the bottom of their respective groups to encourage greater quality control.

Above: The OBO dashboard showing the proportion of ontologies in the OBO Foundry that pass each active principle.

Decisions Made and Important Updates

• The committee proposed enforcing uppercase-only ID space prefixes for new submissions. Proponents argue that this change simplifies downstream tool processing and enhances consistency, while opponents highlight potential impacts on readability and issues with existing mixed-case prefixes. The vote ended 10 to 5 in favor of enforcing upper cases prefixes moving forward. This does not affect any existing ontologies with mixed-case prefixes.

Ongoing Discussions

Here, we list some of the discussions happening around the OBO-sphere:

• The recent meeting of the OBO Operations Committee (OBO Ops) addressed several important topics. A key requirement was emphasized: all OBO Ops members must belong to at least one working group—Editorial, Technical, or Outreach. The potential reorganization of these working groups was discussed to enhance efficiency and collaboration. Members of the OBO Operations team will be asked to reassign themselves to specific working groups, Additionally, the necessity of ensuring that all OBO Ops have clearly assigned tasks was highlighted, aiming to enhance accountability and productivity across the board. A discussion on the appropriate terminology for former members who continue to contribute is in progress to appropriately recognize their ongoing efforts. Additionally, the committee is addressing the issue of incentivizing active participation in working groups, aiming to foster greater engagement and contribution from all members.
• New ontology request issues with no updates from the submitter for more than 2 months will be closed with a standardized message. They can be re-opened by the submitter at any time they are ready to provide updates.

Ontologies

New ontologies accepted in the OBO Foundry Ontology Library \

• SLSO (Space Life Sciences Ontology) (SLSO) is an application ontology designed to support the NASA’s Life Sciences Data Archive and other systems that store space life science research data. The purpose of the ontology is to define and organize the specialized concepts and terminologies used in space life sciences research, which often involves expensive and specialized equipment, procedures, and references to space environments. The SLSO was created using the Ontology Development Kit (ODK) and incorporates concepts from various OBO Foundry ontologies. This allows for the indexing and integration of space biology investigation data with other scientific data related to space environments. The ontology was reviewed by Jie Zheng (see our Spotlight on members below) with active discussion with the maintainer of the ontology.
• AFPO (African Population Ontology) is an ontology that enables the annotation of African individuals and combines knowledge accumulated about existing populations with their genetic fingerprints in a standardized format. AfPO can be employed to comprehensively classify African study participants in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms. The ontology was reviewed by Lynn Schriml with active discussion with the maintainer of the ontology.

New ontologies currently under review

• The Biomarker Ontology (BMO) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). It is being reviewed by Deepak Unni.
• The Physiologically-Based Pharmacokinetics (PBPK) ontology is a comprehensive framework designed to systematically capture and represent the intricate relationships and behaviors of pharmacokinetic processes within living organisms. It is being reviewed by Alex Diehl.

Spotlight on well-established OBO ontologies

In this issue, we continue our ontology spotlight series, highlighting two other ontologies from the OBO Foundry family, Chemical Entities of Biological Interest (ChEBI) and Vaccine Ontology (VO)

• Chemical Entities of Biological Interest (ChEBI) is a freely available, comprehensive database and ontology focused on small chemical compounds of biological relevance. It covers a wide range of molecular entities, including atoms, molecules, ions, and complexes, and provides detailed information on each entity, such as structure, formula, mass, charge, and names. ChEBI uses an ontological structure to organize entities and establish relationships, employing a controlled vocabulary for consistency. ChEBI is semantically integrated with over 100 biomedical ontologies, thus providing powerful capabilities for data integration, hypothesis generation, and reasoning. ChEBI also provides cross-reference links to several other databases and supports interoperability, making it widely used in various fields like cheminformatics, metabolomics, drug discovery, and systems biology. As of June 2024, ChEBI contains 61,325 fully curated entries, establishing it as the leading chemical ontology for life science applications and Semantic Web data annotation. ChEBI can be accessed online and downloaded for research purposes.
• As an OBO library ontology, the Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO systematically standardizes and integrates various vaccines, vaccine components, vaccine mechanisms, vaccine data types, leading to the enhanced computer-assisted reasoning. Dr. Oliver He at the University of Michigan in 2007 initiated the VO development by collaborating with many OBO ontology developers including Drs. Barry Smith, Lindsay Cowell, Melanie Courtot, Bjoern Peters, Alan Ruttenberg, Chris Mungall, Richard Scheuermann, et al. The VO was first presented in the first International Conference of Biomedical Ontology (ICBO), Buffalo, NY, in July 2009 (Ref). Dr. Asiyah Yu Lin later joined He laboratory as a postdoctoral fellow and worked on the VO development during 2010-2014 (Ref). Compared to the 2009-06-08 version of VO that had 2,007 terms, the current VO version as of 2024-06-26 has a total of 14,120 terms, indicating its fast growth. In addition to modeling of vaccines against infectious disease vaccines, the VO has also been expanded to cover non-infectious disease vaccines, including the recently reported cancer vaccines (Ref). The cancer vaccine ontology modeling effort was led by Dr. Jie Zheng who has joined the University of Michigan since 2023 and has been working on this VO project (Jie is featured in our Spotlight on Members below). The VO and VO-related research has been funded by a NIH U24 grant (U24AI171008). In addition, VO has been widely used in many different projects, such as the ImmPort project (https://www.immport.org/), Human Immunology Project Consortium (HIPC) project (https://immunespace.org/), and the Vaccine Adjuvant Compendium (VAC, https://vac.niaid.nih.gov/).

Members and Volunteers

The OBO Foundry is honored to highlight two members who are making valuable contributions to our community:

Jie Zheng

###

Jie Zheng is a software developer and bioinformatician at the University of Michigan, Ann Arbor. She earned her Ph.D. in Biology from Queen’s University (Kingston, Canada) in 2009 and conducted postdoctoral research at the University of Pennsylvania under Dr. Chris Stoeckert, a pioneer in the field of biological ontologies. In 2014, Jie joined the OBO Foundry community and took part in its Operations Committee. She initiated and coordinated the development of the OBO Metadata Ontology to harmonize ontology metadata. Jie has worked on various OBO Foundry ontologies, such as the Ontology of Biomedical Investigations, Occupation Ontology, and Vaccine Ontology. Additionally, she was involved in the development of web-based ontology tools, Ontoanimal (e.g., OntoBee, OntoRat, and Ontodog), in collaboration with Dr. Yongqun “Oliver” He’s team. During her decade-plus working at UPenn, Jie’s focus was primarily on developing ontologies and leveraging them to establish metadata standards, build graph-based knowledge bases, and integrate and analyze data across diverse resources. In 2023, Jie joined Dr. He’s laboratory at the University of Michigan, where she now applies her extensive knowledge of ontologies combined with machine learning techniques to vaccine research.

Damion Dooley

Damion Dooley is an Ontology Development Lead at the Centre for Infectious Disease and One Health (CIDGOH.ca), a 20+ member group of bioinformatics and ontology researchers at the Faculty of Health Sciences, Simon Fraser University, Canada. His ontology work began in 2013 to support rapid enteric pathogen whole genome sequencing and analysis. Damion led the creation of the FoodOn food ontology and the Joint Food Ontology Workgroup to facilitate foodborne disease, agriculture, nutrition and food science data sharing. FoodOn, adopting the many food description facets of LanguaL, a popular food composition thesaurus, is now being used and supported by a wide variety of research and inter-agency data sharing projects. He also participates in The Open Biological and Biomedical Ontologies Foundry operations committee, and in curation of the Ontology for Biomedical Investigations (OBI). He looks forward to a future of FAIR, harmonized data that reduces barriers to discovery and insight in a rapidly changing world.

New Members of the OBO Operations Committee

In this issue we introduce our new member of the OBO Operations Committee. Welcome aboard, Jane Lomax!

Jane Lomax

Dr. Jane Lomax is currently the Head of Ontologies at SciBite, a semantic technology company. In this role, she oversees the development of ontological solutions for clients across various industries, including pharmaceutical R&D, healthcare and consumer goods. She is an advocate for the use of open ontologies and FAIR data principles in industry.

Jane has over 20 years of experience in research, development, and application of ontologies, with former roles with the Gene Ontology and WormBase at EMBL-EBI and the Wellcome Sanger Institute. Jane is an active participant in several public endeavors, she has served on the executive committee of the International Society of Biocuration (ISB), the ELIXIR GCBR Review Committee and presently holds a position on the Pistoia Alliance board.

Jane is a big advocate of the use of public ontologies in industry. At SciBite she supports customers to make best use of them, through both SciBite’s software and services. Jane joined the OBO Operations committee because she feels like there is much to be gained by establishing links between the commercial world and the OBO Foundry, and hopes, by taking up this position, to help facilitate that.

Spotlight on Research in the OBO community

The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies

The Artificial Intelligence Ontology (AIO) is a systematization of artificial intelligence (AI) concepts, methodologies, and their interrelations. Developed via manual curation, with the additional assistance of large language models (LLMs), AIO aims to address the rapidly evolving landscape of AI by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for AIO includes AI researchers, developers, and educators seeking standardized terminology and concepts within the AI domain. The ontology is structured around six top-level branches: Networks, Layers, Functions, LLMs, Preprocessing, and Bias, each designed to support the modular composition of AI methods and facilitate a deeper understanding of deep learning architectures and ethical considerations in AI.

(Figure from Joachimiak M p., Miller MA, Caufield JH, Ly R, Harris NL, Tritt A, Mungall CJ, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. 2024 Apr 3; http://arxiv.org/abs/2404.03044)

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis

This work by Zheng et al (Jie Zheng was also featured above in the OBO Member Spotlight) is about the development of an ontological model for cancer vaccines using the Vaccine Ontology (VO) to facilitate standardization, integration, and analysis of heterogeneous cancer vaccine data. The authors used various ontologies and tools from the Open Biomedical Ontologies (OBO) Foundry to develop a comprehensive ontological model for cancer vaccines within the Vaccine Ontology (VO). They followed OBO Foundry principles by reusing terms from existing ontologies such as the Human Disease Ontology (DOID), NCBITaxon, and the Ontology for Biomedical Investigations (OBI). Tools like ROBOT and the Ontology Development Kit (ODK) were used to extract relevant terms, automate ontology workflows, and ensure adherence to OBO guidelines. With this approach, the authors created a Cancer Vaccine Ontology (CVO) that standardizes diverse cancer vaccine data, supports ontology-based analysis of vaccine attributes and clinical trials, and facilitates data integration and knowledge discovery.

(Figure from Jie Zheng, Xingxian Li, Anna Maria Masci, Hayleigh Kahn, Anthony Huffman, Eliyas Asfaw, Yuanyi Pan, Jinjing Guo, Virginia He, Justin Song, Andrey I. Seleznev, Asiyah Yu Lin & Yongqun He. 2024 June 19 https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-024-00312-3

Spotlight on OBO Principles

In this issue, we continue with Principle 4 of the OBO Foundry’s series of principles.

OBO Foundry Principle 4: Versioning

Principle 4 specifies the requirements for versioning. The ontology provider must have well-documented procedures in place for versioning the ontology. Each official release of the ontology must be clearly marked with a unique version identifier, which should be in one of two formats: either a date format following the “YYYY-MM-DD” pattern or a numbering system such as semantic versioning (e.g., “NN.n”).

Every released version must have a unique IRI version that resolves to the specific ontology artifact associated with that version. The IRI must contain the same version identifier as the artifact itself to ensure consistency. It is recommended that version IRIs use dated PURLs to ensure long-term accessibility.

Once an official version of the ontology is released, the content of the released files must not be altered. If any bugs or issues are discovered in a released version, they should not be fixed by modifying the existing files. Instead, the fixes should be incorporated into a new official release with its own unique version identifier and corresponding files.

Additionally, the ontology should include an owl:versionInfo statement that matches the version identifier used in the IRI and the artifact.

Fixing common problems

The automatic check that is performed as part of the OBO Dashboard is implemented here. Roughly half of the ontologies in the OBO Foundry currently pass this check. While there are some ontologies that do not contain a correctly formatted version IRI, the most frequent problem is that an existing version IRI does not resolve correctly. A typical solution to this is to ensure that an appropriate rule (see, for example, PATO) for redirecting from GitHub is defined, and then use GitHub releases as a way to create “tags”. For example, when the March 2024 release of PATO was created (https://github.com/pato-ontology/pato/releases/tag/v2024-03-28), it was created using the “tag” v2024-03-28 (note the leading “v”). This tag works very similar to a branch, and you can actually browse the GitHub repository for that tag (https://github.com/pato-ontology/pato/tree/v2024-03-28). In summary, for 90% of the problems:

1. Make sure you have a correctly formatted version IRI that is updated with ever release
2. Every time you create a release, you also create a GitHub release
3. The purl config redirects the version IRI to the GitHub tag (as shown in the PATO example above)

Spotlight on Tools: Recent updates

Special announcement to the entire OBO community since we’ve had not one, not two, but three software releases of interest in the past few days:

ROBOT 1.9.6: In the latest update, several additions and changes have been made. The duplicate exact synonym report query has been updated to be case-insensitive and to ignore synonyms annotated as abbreviation or acronym synonym types (#1179). The –drop-axiom-annotations option has been extended to support value-specific removal of axiom annotations (#1193). The obographs have been updated to version 0.3.1, and the OWL API has been upgraded to version 4.5.29, which includes a major update to the OBO Format, now supporting IDSPACE declarations for non-OBO Foundry prefixes. The Elk reasoner has also been updated to version 0.6.0.

ODK 1.5.1: In the ODK toolbox, ROBOT has been updated to version 1.9.6 (see above). It also includes an updated version of the Elk reasoner and long-awaited prefix map support for the OBO format.

Protégé 5.6.4: For better interoperability, this minor release uses the same latest OWLAPI version as the one used in ROBOT 1.9.6, and the same latest ELK reasoner as well. It fixes a few bugs, makes the support for ID range policy files more flexible, and adds a new setting to configure which explanation plugin(s) should be used.

Spotlight on Tools: Ontology Browsers

Here and in upcoming issues of this newsletter, we would like to highlight some key browsers in the ontology community: the Ontology Lookup Service (OLS), Ontobee, and BioPortal. These browsers are essential for navigating and utilizing the support of ontological data available. We spotlight OLS in this issue; watch for spotlights on Ontobee and BioPortal in future issues.

Ontology Lookup Service (OLS)

The Ontology Lookup Service (OLS) is a critical tool for the OBO Foundry community, providing a comprehensive and user-friendly interface for accessing and searching a wide array of OBO ontologies. OLS simplifies the process of exploring and integrating ontological data by offering a centralized platform where users can browse, query, and visualize terms across multiple OBO Foundry ontologies. With its API and advanced search capabilities, OLS enables researchers and developers to efficiently retrieve relevant information and incorporate ontological knowledge into their applications. OLS continues to support the OBO Foundry community in managing and utilizing vast amounts of structured data effectively.

Events

• ICBO 2024 in the Netherlands
  • The OBO Foundry Tutorial at ICBO will focus on collaborative workflows and leveraging freely available online training resources. Attendees will learn strategies for maintaining community-based ontologies in a distributed development environment. The goal of the tutorial is to provide insights into the latest updates and best practices in ontology development. Here are some key topics that will be covered:
    • Managing ontologies built and maintained by volunteers and dispersed teams
    • Utilizing GitHub for issue tracking, documentation, discussions, automation pipelines, and highlighting social workflows
    • Adhering to open science principles

    The tutorial will have a “show and tell’’ format to encourage real-time participation. Attendees are encouraged to install the following software in advance: GitHub Desktop, Protégé, and ROBOT. The tutorial is organized by Nico Matentzoglu from Semanticly and Nicole Vasilevsky from the Critical Path Institute.

• COB Workshop: Purpose: To advance the development of COB.
  • The COB Workshop will be held at the La Jolla Institute for Immunology (9420 Athena Cir, La Jolla, CA 92037) on September 23-24, 2024. Register for the workshop at https://forms.gle/QZetUv2VhPhM3Rqq6.
  • Both in-person and virtual attendees are required to complete the registration form in order to receive additional information.
• OBO Academy: Monarch Seminar Series (ongoing)
• The OBO Academy: Monarch Seminar Series has been moved to a monthly cycle until further notice. The next seminar on 2024/07/23 will be a follow up session on the ICBO tutorial above, see schedule below. After that, OBO Academy will go into a summer break, and we will resume 2024-09-17 (topic tbd).
• Schedule: https://oboacademy.github.io/obook/courses/monarch-obo-training/
• You can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Recent OBO Academy seminars

• Introduction to the Uberon Anatomy ontology (Damien Goutte-Gattat (FlyBase) and Nico Matentzoglu)
• An Introduction to Synonyms in OBO Ontologies (Nicole Vasilevsky, C-Path)
• AI-assisted ontology editing workflows 2: Validation (Chris Mungall, LBNL)
• Phenotype data and the role of ontologies (James McLaughlin (EBML-EBI) and Nico Matentzoglu)

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list (low-traffic, no spam)
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace (when you join the obo-discuss mailing list, the welcome message has an invitation link for the Slack workspace).
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are various roles in which you can contribute, including assisting with the production of this newsletter

Well into the new year, we are happy to present the 4th issue of the OBO Foundry newsletter.

This edition highlights two great contributors, Anita Caron, and Bill Duncan, and two well-established ontologies, OccO (the Occupation Ontology) and FoodOn. Additionally, we shine a light on two new members of the OBO operation committees, James Stevenson and Vinicius de Souza.

Several ontology reviews are underway, with constructive dialogues aligning with OBO Foundry standards. We also summarize two research studies published by members of the OBO community.

Like spring’s renewal, our community grows through collaboration. We remain committed to creating usable, interoperable ontologies to advance biomedical research. With much potential still unfolding, we look forward to continued growth and contributions!

Happy spring season! We are looking forward to great things in bio-ontology!

Best regards, The OBO Foundry Operations Committee.

Highlights

OBO Dashboard Compliance is Live Now

With the arrival of 2024, mandatory compliance with the OBO Dashboard is now in effect. The OBO Foundry will soon be showing a visual indicator on the homepage to display each ontology’s compliance status. Non-compliant ontologies will be sorted and shaded at the bottom of their default ontology-by-topic view group. This will serve as an informative measure for users and encourages ontology curators to strive for quality control.

Remember, only dashboard errors (black X on a red background) cause non-compliance. Warnings (yellow triangle) or information (blue i) in the final ‘Summary’ column are still acceptable. Ontologies in the dashboard are sorted by Dashboard status, which means that ontologies without errors are shown first: https://dashboard.obofoundry.org/dashboard/index.html.

An explanation of the dashboard report is available here (link to dashboard video); more information can be found at http://dashboard.obofoundry.org/dashboard/about.html.

Decisions Made and Important Updates

• Addition of a new ontology status: “unresponsive”, which signifies that the ontology project does not have a contact person who is responsive, but the ontology is still being actively maintained.
• New Ontology submissions no longer need to pass the criterion “resolvable version IRI” during the submission process, as this is tied to the PURL resolution system. It is, however, expected that when an ontology is officially admitted, the version IRI does resolve correctly,
• Updating the SOP document to include a new subsection under “Reviewing Ontologies for OBO Membership.” This subsection, titled “Rules of Communication,” designates the official ontology reviewer as the authority to decide which community suggestions need to be addressed and which do not, aiming to manage situations where community input might not meet the established principles. This addition is intended to streamline the review process and clarify the role of community feedback in ontology evaluations. For more details, please visit the pull request page #2528
• The EWG improved the OBO Foundry ontology review process by specifying how community input should be taken into account during the review process. The Ontology reviewer has the last word, and is responsible to communicate which feedback is optional, and which mandatory to be addressed before admission (Issue #2459).
• The EWG created an improved FAQ about the OBO Dashboard, covering its role in the Ontology Review process and guides on how to address specific issues. (Issue #2263)

Ongoing Discussions

Here, we list some of the discussions happening around the OBO-sphere:

• The OBO Foundry team is considering implementing lexical matching in their review process for new ontology requests. This method would use a script to identify any content overlaps with existing ontologies, aiming to preserve the distinctiveness and compatibility of ontologies in the Foundry. The discussion focuses on developing an automated script for overlap detection, addressing potential inaccuracies, and enhancing the efficiency and precision of the review procedure. Join the discussion.
• Discussion about adding a metadata field to ontologies that links to annotations, such as text mining corpora and gene associations, to facilitate easier navigation for ontology users. This aims to address challenges in accessing information about the use of ontologies in various datasets, including details on versions, subsets used, and curation practices. A suggested format for this metadata includes identifiers and URLs for annotated datasets. Join the discussion.
• A testable solution for supporting prefix declarations in OBO format has been provided by Jim Balhoff. Please help out with testing this important change!: https://github.com/owlcs/owlapi/pull/1102#issuecomment-1924073439

Ontologies

Reviewing Ontologies for OBO Membership

We recently updated the Standard Operating Procedure (SOP) for Ontology Acceptance/Rejection Decision. The reviewer presents their assessment and recommendation regarding a new ontology to the OBO Operations Committee. The committee may request clarifications from the reviewer before making a decision on the ontology’s acceptance. The decision is made by consensus among the attendees on the call, meaning no strong objections are raised. There is no minimum number of attendees required for the decision to be made.

Ontology Acceptance Notification

The ontology reviewer should notify the ontology owner about their ontology’s acceptance, both in the ticket and via email (copying obo-discuss & obo-operations-committee), using a provided template. The template informs the owner about the next steps, which include creating a metadata record for their ontology in the OBO Foundry GitHub repository and creating a PURL registry entry. The metadata record should be based on the curated metadata from the obo-nor.github.io repository, and the pull request for adding the record should include a link to the New Ontology Request issue. The ontology owner is also provided with examples of a metadata record and a PURL yml file.

New ontologies accepted in the OBO Foundry Ontology Library

• The Gall Ontology. The GALLONT submission to OBO Foundry, discussed in GitHub issue #2522, proposes an ontology for plant gall phenotypes. It aims to provide a controlled vocabulary for describing plant galls, integrating terms from PATO, PO, and other OBO ontologies. The ontology has been formally accepted and is now included on obofoundry.org.

New ontologies currently under review

• The Space LIfe Sciences Ontology The Space Life Sciences Ontology (LSDAO) submission for OBO Foundry inclusion supports NASA’s Life Sciences Data Archive and related systems, offering definitions and organization for space life science research data. It integrates concepts from several OBO Foundry ontologies and the Science Data Discovery Ontology for broader research applicability. Ongoing discussions focus on refining LSDAO for clarity, accuracy, and OBO Foundry compatibility. Join the discussion.

Spotlight on well-established OBO ontologies

In this issue, we continue our ontology spotlight series, highlighting two other ontologies from the OBO Foundry family. Occupation Ontology (OccO) and Food Ontology (FoodOn)

• Occupation Ontology (OccO) is a reference ontology in the domain of human occupations. It is designed to ontologize and harmonize the occupation classification from many existing occupation standards, including the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications, and Occupations (ESCO) of the European Union. Currently, the ontology contains over 1,600 occupations, encompassing all US SOC occupations. In addition to occupations, the ontology also defines skills, abilities, and credentials highly related to the occupations. One ongoing OccO use case study aims to facilitate the Alabama government’s Talent Triad initiative, which connects individuals, employers, and credential providers using a common skills-based occupation framework. OccO was initiated by Sam Smith and Oliver He at the University of Michigan Medical School, Ann Arbor, MI, USA, in 2018, and since then has involved more ontology developers and domain experts from the University at Buffalo, Simon Fraser University, and the US Alabama Commission on Higher Education, among others. OccO has been presented at many meetings, including OSS2022, ICBO2022, and OSS2023. The ontology was accepted as a member of the OBO Foundry library ontologies in 2023. OccO is actively developing with weekly development calls and continuously seeks collaborators to contribute to the ontology.
• Food Ontology (FoodOn) is an ontology of over 35,000 classes focused primarily on naming kinds of food material for human and domesticated animal consumption. This includes both plant, animal and fungal material as well as inorganic chemicals. Terms for many foundational “single organism” food materials include details of taxonomic category, anatomical part, and even life cycle. As well, thousands of common (non-brand name) multi-component food products are included. Vocabulary to describe food characteristics and processing steps, as well as other contextual facets to describe packaging, dietary pattern, nutritional term hierarchy, and agricultural source are provided. To maximize FAIR data interoperability, FoodOn imports from UBERON, the Plant Ontology, ENVO, ChEBI, the Ontology for Nutritional Studies, and the OBO Relations ontology, among others. In addition to using FoodOn to describe food composition of meals in a “bag-of-terms’’ way (FoodOn was derived from LanguaL, a longstanding food composition database thesaurus), the ontology can be used like a grammar to construct graph knowledge base statements about food which can be queried or reasoned with. For global resource integration, mapping to USDA nutrition databases such as Foundation Foods and SR Legacy is underway, as well as the European EFSA FoodEx2 vocabulary. For more information and opportunity to participate, see ongoing development and ontology design information at www.foodon.org and the GitHub repository.

Members and Volunteers

The OBO Foundry is honored to highlight two members who are making valuable contributions to our community:

Anita Caron

Anita Caron has been a Semantic Web Developer at the European Bioinformatics Institute (EMBL-EBI) since 2021 as part of the Samples, Phenotypes, and Ontologies (SPOT) team. She is deeply involved in technical improvements across many ontologies, such as Uberon, Cell Ontology, and Relation Ontology (RO) which are crucial components to the Human Reference Atlas (HRA), part of the Human BioMolecular Atlas Program (HuBMAP). She also has contributed to developing the most recent versions of the Ontology Development Kit (ODK). Passionate about advancing metadata standardization, her contributions extend beyond ontology development, as she actively participates in organizing tutorials to educate and empower other ontology developers on best practices in metadata standardization and quality control. More details are in the section “Recent OBO Academy seminars”.

Anita holds an important role at OBO Foundry as the OBO Dashboard Maintainer. She is entrusted with the responsibility of maintaining and releasing the OBO Dashboard, a key resource for the community.

Bill Duncan

Bill Duncan is an AI researcher and faculty member at the University of Florida College of Dentistry. He has been involved in the OBO Foundry for more than a decade and is the lead developer of the Oral Health Disease Ontology (OHD). In addition to the OHD, Bill has contributed to several OBO Foundry ontologies over the years, such as the Relation Ontology (RO), Environment Ontology (ENVO), Ontology for General Medical Science (OGMS), Ontology for Modeling and Representation of Social Entities (OMRSE), Occupation Ontology (OCCO), and the UBERON multi-species anatomy ontology (as well as others). He is also currently working on non-OBO Foundry ontologies. These include the Pain Ontology and the Neural Interface Ontology, an ontology for representing devices that augment the nervous system, such bionic vision devices and cochlear implants.

As a bioinformatician, Bill has been involved in a number of clinical studies in the dental and cancer domains. In the dental domain, he has been an innovator in the use of private-practice dental records to study dental treatment outcomes, such as root canals and tooth restorations. In the cancer domain, he has been involved in studies to assess the role that the circadian rhythm plays in mitigating oral mucositis in oral-cancer patients undergoing radiation therapy, and how variations in a patient’s chemotherapy regimen affects the treatment of ovarian cancer. Prior to joining the University of Florida, Bill was an ontologist and software developer for the National Microbiome Data Collaborative, which aims to promote microbiome research through the development of data standards that enable the sharing of microbiome research data.

Outside of work, Bill enjoys time with his family and plays a mean game of pickleball 😊

New Members of the OBO Operations Committee

In this issue we introduce two volunteers that recently joined the OBO Operations Committee. Welcome aboard Vinícius de Souza and James Stevenson! James will take over the role of OBO Website Coordinator from Erik Whiting who has served in that role for over a year now. Thank you for all your work, Erik!

Picture	Name	GitHub	Affiliation	Country	Role
	Vinícius de Souza	@souzadevinicius	EMBL-EBI	UK	Technical Working Group OBO Operations - OBO Website
	James Stevenson	@jsstevenson	Nationwide Children’s Hospital (Columbus, OH)	USA	OBO Website Coordinator

Spotlight on Research in the OBO community

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

This preprint introduces “Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI),” a method that employs Large Language Models to automate the creation of ontological components. Aiming to simplify the complex process of ontology development in fields like biomedical and environmental sciences, DRAGON-AI was tested on ten diverse ontologies, showing its efficacy in producing accurate relationships and definitions. Despite its potential to streamline ontology construction, the research emphasizes the critical need for domain experts to refine AI-generated outputs to ensure their precision and reliability. Thus, DRAGON-AI marks a pivotal move towards blending AI with human expertise to facilitate more efficient and effective ontology maintenance and development.

Figure 1. DRAGON-AI approach

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

The paper presents “SPIRES,” a novel approach for populating knowledge bases using Large Language Models (LLMs) without needing extensive training data. Utilizing LLMs’ zero-shot learning capabilities, SPIRES extracts information that fits a predefined knowledge schema through recursive structured prompting. This method enables the extraction of complex data structures and improves accuracy by aligning entities with existing ontologies. Demonstrated across various domains like food recipes and disease treatments, SPIRES offers accuracy comparable to traditional methods but excels in entity grounding. It highlights the method’s flexibility, ease of use, and ability to adapt to new tasks, promoting LLMs’ role in knowledge curation. SPIRES is part of the open-source OntoGPT package, facilitating its adoption and adaptation for different knowledge extraction tasks. This approach represents a significant step forward in using AI and NLP technologies to efficiently and accurately assemble knowledge bases, offering a scalable and adaptable tool for researchers and organizations dealing with large volumes of unstructured information.

Figure 1. Overview of the SPIRES approach. .

Spotlight on OBO Principles

In this issue, we continue with Principle 3 of the OBO Foundry’s series of principles.

The OBO Foundry emphasizes the importance of interoperability by requiring ontologies to use standardized IRIs, as outlined in Principle 3. This ensures ontologies are easily accessible and identifiable on the web, promoting seamless integration and use across different platforms and systems.

OBO Foundry Principle 3: URI/Identifier Space:

The OBO Foundry insists on unique IRIs, designated as PURLs, to ensure ontologies are easily identifiable and accessible online, incorporating approved, concise namespaces.

This requirement facilitates the prompt identification of ontology elements, in line with OBO Foundry’s ID policy, enhancing standardization and web presence of ontological data. Compelling proper IRI structures for ontologies and their components highlights the criticality of adhering to established guidelines.

An automated verification mechanism checks that namespaces are duly registered and IRIs precisely follow specified formats, supporting consistency and ensuring broad compliance across the ontological spectrum.

Spotlight on Tools

A major release (1.5) of the Ontology Development KIT (ODK) was published after more than a year of development, with significant contributions from members of the OBO Technical Working group (Blog post). Some highlights include the introduction of the “International Release” and a complete workflow system for ontology internationalization, the redefinition of “Base Release”, a fundamental piece of our vision for decentralized ontology development and added support for ROBOT plugins, which supports the inclusion of custom ROBOT plugins in your ODK workflows.

Events

OBO Academy: Monarch Seminar Series (ongoing)

• Tutorial 2024/04/02: Synonym Type curation - a deep dive
• Tutorial 2024/04/16: AI-assisted ontology editing workflows 2

Don’t forget you can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Recent OBO Academy seminars

• Harry Caufield from Lawrence Berkeley National Laboratory discussed the Bridge to AI (Bridge2AI) data standards developed to make biomedical and biological data AI-ready. He covered the challenges in determining data AI-readiness, the Bridge2AI standards registry using LinkML, the importance of structuring data and metadata, the development of the “Data Sheets for Datasets” (D4D) schema, efforts to align Bridge2AI standards with existing standards, and suggestions for biocurators and ontologists to contribute to making data AI-ready. The presentation emphasized the importance of developing standards and tools to unify data attributes, making data more accessible, reliable, and suitable for AI-driven methods in biomedicine. The tutorial was called “Bridge2AI data standards: a practical introduction” and the recording can be accessed here.
• In this OBO Academy training session, Anita Caron from EMBL-EBI presented the importance of ontology metadata standardization for building an interoperable knowledge graph in the biological and biomedical domains. She highlighted the challenges of integrating diverse ontologies and the need to use standardized annotation properties. She introduced tools for ontology metadata validation, such as ROBOT reports, custom SPARQL queries, and the OAK Validate tool. Anita also discussed the Ontology Metadata Model, a LinkML schema for the ontology metadata. She emphasized the need for further discussion and agreement on metadata standardization practices within the OBO community to enable development of interoperable ontologies for the life sciences. The tutorial was called “Ontology Metadata Standardisation” and the slides can be accessed here. The recording is here.
• Chris Mungall demonstrated AI-assisted ontology editing workflows using large language models (LLMs) like ChatGPT and Claude. He showcased capabilities such as review-based workflows to identify errors, enhancement workflows to fill in missing information, and utilizing plugins for generating ontology terms and searching the literature. Chris discussed the pros and cons of LLMs in ontology curation, the need for human oversight, and the potential of using tools like Curate GPT to improve reliability. The presentation encouraged the OBO community to explore and share experiences in this emerging field. The tutorial was called “AI-assisted ontology editing workflows, Part 1” and the slides can be accessed here. The recording is here.

Updates on past events

• The 17th Annual International Biocuration Conference was held in Faridabad, India from March 5-8th, 2024. Several active members of the OBO community attended the event, as well as a large delegation of Indian researchers and students who use OBO Foundry ontologies in their work. Many of the Indian delegates work in agriculture and crop sciences and use OBO Foundry ontologies for the annotation of genotypes, metabolites, and phenotypes in their work to increase crop yields, nutritional value, and decrease disease. Charles Tapley Hoyt wrote a blog post (https://cthoyt.com/2024/03/11/biocuration2024-discussions.html) summarizing some of his personal experiences at the conference. \

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list (low-traffic, no spam)
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace (when you join the obo-discuss mailing list, the welcome message has an invitation link for the Slack workspace).
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are various roles in which you can contribute, including assisting with the production of this newsletter

Season’s Greetings from the OBO Foundry Community!

As we wrap up another year with many developments in and around bio-ontologies, we are excited to present the third edition of the OBO Foundry Newsletter during this festive season. In the spirit of celebration and reflection, we want to thank the entire OBO community for their continued dedication and contributions.

In this edition, we will share highlights of the achievements and milestones reached throughout the year. From collaborative projects to individual accomplishments, we aim to showcase the collective success of our community. We will shine our spotlight on two long-standing OBO Foundry members, Nomi Harris and James Overton, and two ontologies, the Uberon anatomy ontology and the recently renamed Ontology for Modeling and Representation of Social Entities (OMRSE).

Wishing you a joyful holiday season and a prosperous New Year filled with exciting developments in the bio-ontological world!

Best regards, The OBO Foundry Operations Committee.

Highlights

OBO Foundry 2023: Year at a Glance

This is a spotlight summary of the key developments for the OBO Foundry in 2023:

• New ontologies were added after a review process, including: MCRO, VBO, NGBO, ADO and OCCO.
• A decision was made to mandate OBO Dashboard validation starting in January 2024. At first, this will result only in presentational consequences on the website.
• Community outreach was strengthened through newsletter relaunch and member surveys.
• Technical infrastructure was upgraded through ROBOT, ODK, and PURL server improvements.
• Discussion began about the possibility of starting a nonprofit organization to support work on OBO Foundry.

2023 was a year of important decisions and advances for OBO Foundry. The mandatory dashboard validation and increased focus on community outreach will support future improvements.

Important Reminder: OBO Dashboard Compliance in 2024

As we approach the third edition of our newsletter, we wish to remind the OBO community that, starting January 1^st, 2024, passing the OBO Dashboard will be mandatory. The OBO Foundry will introduce a visual indicator on the OBO Foundry homepage to display each ontology’s compliance state. Non-compliant ontologies will be sorted and shaded at the bottom of their default ontology-by-topic view group. This serves as an informative measure for users and encourages ontology curators to strive for excellence in quality control.

Remember, only dashboard errors (black X on a red background) cause non-compliance. Warnings (yellow triangle) or information (blue i) in the final ‘Summary’ column are (still) acceptable.

An explanation of the dashboard report is available here (link to dashboard video); more information can be found at http://dashboard.obofoundry.org/dashboard/about.html.

Decisions Made and Important Updates

• Claudia Sánchez-Beato Johnson started a discussion with a request to add a “has_acronym” property to OMO. The debate centered on whether acronyms should be a distinct property or follow the “synonym type” pattern. Consensus at the OBO Foundry Operations Committee meeting led to the addition of a new ‘acronym’ synonym type in OMO. The decision avoided introducing a separate ‘has_acronym’ property to maintain consistency and prevent disruptions to existing tools.

Ongoing Discussions

Here, we list some of the discussions happening around the OBO-sphere:

• Criteria and process for marking ontologies as inactive, unresponsive, orphaned, etc. The OBO Operations Committee is working to define these different status labels clearly. Join the discussion.
• The movement to standardize synonym types (e.g. abbreviation, UK spelling, layperson) across OBO Foundry ontologies is ongoing. Join the discussion or find a list of the current synonym types on ontobee.
• The potential need for paid staff to accelerate progress is being considered as part of a discussion on whether the OBO Foundry should transition to a non-profit organization (join the discussion if you have experience and would be able to help out).
• Related to the above, a discussion on OBO Foundry’s governance practices led to recommendations for enhancing governance by defining the community, establishing a steering committee, documenting decision-making, improving conflict resolution, ensuring consistent policies, and creating SOPs for ontology status. The ultimate goal is to strengthen governance, enabling funding applications, priority oversight, community engagement, and potential non-profit transition, while acknowledging the required effort. The aim is to enhance transparency, equity, accessibility, and community participation in OBO Foundry’s activities.

Ontologies

Reviewing Ontologies for OBO Membership

The Standard Operating Procedure (SOP) for reviewing ontologies outlines the criteria for a comprehensive yet time-efficient manual review of ontologies submitted for registration with the OBO Foundry. There are four roles involved in the review process:

• The “submitter” is the individual who originally submitted the request for OBO Membership and the point of contact on behalf of the ontology.
• The New Ontology Request (NOR) Manager, a specific role in OBO currently held by Paul Fabry, is responsible for guiding the submitter through the submission process and performing the initial review of the ontology, which includes ensuring that the submission request is completed appropriately and that the ontology is validated in the OBO Dashboard.
• The OBO Foundry reviewer is the primary reviewer assigned by the OBO Operations Committee to perform the in-depth review of the ontology.
• The OBO community is any member of the community that wishes to contribute to the full open review of the ontology. While feedback by the community is welcome, the OBO Foundry reviewer is ultimately responsible to decide which feedback affects the membership decision.

The review focuses on key aspects such as ontology scope, adherence to the OBO identifier scheme, accurate use of imported terms, appropriate axiomatic patterns, and correct application of object properties. The SOP underscores the importance of demonstrating the ontology’s relevance to life sciences, using expert input, and justifying any overlaps with existing terms. Submitters are expected to be willing to address identified issues within two months. Once the OBO Foundry reviewer reaches a decision, the decision is presented to the OBO Foundry Operations Committee, and unless there is a veto from any of the committee members, the ontology is either accepted or rejected.

Ontologies currently under review

• The Caroli’s Disease and Syndrome ontology. CaroliO, focusing on Caroli’s Disease and Syndrome, has been submitted for inclusion in the OBO Foundry ontologies. The ontology aims to improve the diagnosis and treatment of these rare liver conditions. It offers a structured representation of symptoms, outcomes, and treatment options, supporting researchers and healthcare professionals in advancing their understanding and strategies. CaroliO is currently under review; the contributors are actively addressing feedback and making necessary updates to enhance the ontology’s quality and alignment with OBO Foundry standards. Join the discussion
• The African Population Ontology (AfPO) was developed to comprehensively classify African study participants in prospective research studies. CaroliO is currently under review. Join the discussion.

Spotlight on well-established OBO ontologies

In this issue, we would like to highlight two ontologies from the OBO Foundry family: Uberon multi-species anatomy ontology and OMRSE.

• Uberon multi-species anatomy ontology is a comprehensive species-neutral ontology that aims to represent anatomical structures consistently across a wide range of taxa. Uberon incorporates extensive connections to taxon-specific anatomical ontologies, facilitating the integration of expression, function and phenotypic data. The ontology currently contains over 16,000 terms covering structures found across various metazoans and integrates with other ontologies, such as the Cell Ontology (CL) or the Gene Ontology (GO). Uberon was released in 2012, and soon thereafter became part of the OBO Foundry. The ontology is constantly expanding with new terms and relations thanks to volunteer editors, developers and users that provide constant feedback. In the last few years, programs like HuBMAP have contributed not only to expanding and refining Uberon, but also to integrating 3D reference objects and 2D reference functional tissue units.

• The Ontology for Modeling and Representation of Social Entities (OMRSE) is an ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. OMRSE, formerly known as the ‘Ontology of Medically Relevant Social Entities,’ has recently been renamed the ‘Ontology for Modeling and Representation of Social Entities’. This change reflects its broader scope encompassing all entities emerging from human social interactions, such as roles in organizations, households, education, language, and money. The primary reasons for the change were to clarify its domain and acknowledge that most social entities are medically relevant, addressing concerns within the OBO (Open Biomedical Ontologies) community. This shift was initiated during discussions with the Occupation Ontology (OccO) team, particularly regarding the representation of occupations and their related social entities.

  Implementing the name change was complex, involving updates across various platforms, including OBO metadata, the OMRSE GitHub site, OWL artifacts, and more. The OMRSE team carefully planned this transition to ensure simultaneous updates across all channels. Despite the change, the acronym OMRSE and its OBO ID remained the same to maintain stable identifiers. The revision process also provided an opportunity to update documentation and references on the GitHub site. Overall, this consensus-driven name change aimed to enhance clarity and facilitate better categorization of social entities within the OBO framework and was executed smoothly thanks to thorough preparation.

Members and Volunteers

The OBO Foundry is excited to spotlight James A. Overton and Nomi Harris in the third issue of our newsletter.

James Overton is a longtime member of the OBO community and has made significant contributions as a leading member of the OBO Foundry Technical Working Group. His work has had a lasting impact on the OBO community and beyond.

Nomi Harris is a dedicated OBO member who has been vital to the community for many years. She has played an instrumental role in organizing issue trackers, editorial work, and general cat-herding.

Nomi Harris

Nomi Harris is a Program Manager for the Berkeley Bioinformatics Open-Source Projects (BBOP) group at the Lawrence Berkeley National Laboratory. The group is led by Chris Mungall, who is well known in the ontology world and was one of the co-founders of OBO. Nomi has a master’s degree in computer science from MIT, and wrote bioinformatics software for years before transitioning to project management. She has been involved with the OBO Foundry since 2007.

In addition to coordinating about a dozen projects for BBOP, Nomi chairs the annual Bioinformatics Open Source Conference (BOSC) and is on the Boards of the Open Bioinformatics Foundation and the International Society for Computational Biology (ISCB, the organization that runs the ISMB conference). In her spare time, she leads a quartet that sings Renaissance music for fun; co-leads a folk music song circle; and fosters kittens.

James A. Overton

James builds open source software for open science, and OBO is fundamental to his work. Through his consulting company Knocean, he works for various scientific databases and ontology projects across our community. Since completing his PhD in 2012, James has worked with Bjoern Peters and Randi Vita at the La Jolla Institute on many projects that apply ontologies to immunology, including the Immune Epitope Database, clinical and biological databases for COVID, standards development for ImmPort and ImmuneSpace, and the new HIPC Coordinating Center. He has also worked for the National Toxicity Program’s Chemical Effects in Biological Systems database for many years, for the Gene Ontology on tools for ontologies such as ROBOT, with the Critical Path Institute on documentation such as the OBO Academy, and projects for the European Bioinformatics Institute and various universities. James is best known for leading the development of open source software that helps all of OBO, including ROBOT (the ontology automation tool), the OBO PURL system, the OBO Dashboard, and is hard at work on the next generation of open tools for open science.

Spotlight on Research in the OBO community

Open code, open data, and open infrastructure to promote the longevity of curated scientific resources

In light of the widespread issue of curated scientific resources becoming out of date, abandoned, or inaccessible, Charles Tapley Hoyt and Benjamin M. Gyori propose the Open Code, Open Data, and Open Infrastructure (O3) guidelines as an actionable roadmap towards promoting the longevity and sustainability of such resources. The O3 guidelines cover three aspects:

1. Technical Aspect: make code and data open, version-controlled, permissively licensed, and approachable to contributors. Build on open infrastructure to enable automation of quality control, release, and other technical workflows.
2. Social Aspect: use public collaborative tools like GitHub for issue tracking, discussion, and code/data review. Emphasize community engagement by building training materials, curation guidelines, and instituting a welcoming code of conduct.
3. Governance Aspect: establish a minimal governance model early, distribute authority across institutions, codify a liberal attribution policy, and encourage transparent discussion.

Figure 1. A schematic diagram of how social workflows, technical workflows, and project governance interact with the open data, open code, and open infrastructure (O3) guidelines.

The authors suggest that implementing the O3 guidelines enables increased community participation, better highlights individual and institutional contributions, promotes inclusivity, and reduces financial and time burden on maintainers. In turn, these can mitigate the risks of the fluctuation in personnel, funding, and institutional priorities, reduce overlapping curation efforts, broaden opportunities for contribution, and ultimately create better resources.

While not (yet) endorsing the O3 principles directly as part of our own recommendations, the OBO Foundry is deeply committed to improving technical, social and project workflows in the spirit of the proposal.

Watch a related presentation by the authors from the Biocuration 2023 Conference.

Spotlight on OBO Principles

In this issue, we continue with Principle 2 of the OBO Foundry’s series of principles. The OBO Foundry has established these principles as best practices for creating usable, sustainable, and interoperable ontologies. Each principle serves as a criterion for evaluating the potential inclusion of new ontologies. Starting with Principle 1 in a previous newsletter, we now explore Principle 2 in this edition.

OBO Foundry Principle 2: Common Format:

The OBO Foundry pursues interoperability at four different levels (Figure 2). In the last newsletter, we talked about the importance of the “Open” principle (layer 4 in Figure 2 below), which mandates a standardized open license for all OBO ontologies. Today, we are going to remind you about the importance of supplying ontologies in a “common format” (layer 3 in the Figure), as specified by Principle 2.

A format comprises two components: a data model (like OWL, SKOS, or RDFS) and a serialization (RDF/XML, OBO Format, Functional Syntax). Over the course of the last 20 years, the OBO Foundry has promoted the use of the OWL model for representing ontologies, mapping other standards like the OBO Format, which is used by a large number of ontologies, to OWL and writing standard “converters” to translate between the two. But using a common data model is not all that is needed: if ontologies are distributed in different serializations, interoperability is hampered because most tools do not provide parsers for all serializations (with the exception of the OWL API). To maximize uptake across various communities of practice, the OBO Foundry mandates the RDF/XML standard as the main serialization for OWL ontologies, making it possible to process ontologies using a wide variety of standard RDF tools as well as specialized OWL tools. The Common Format principle therefore ensures that all primary ontology releases must be serialized in RDF/XML.

The implementation of the “Common Format” principle has been one of the most successful OBO principles, with only a handful of ontologies in the Foundry failing to provide an RDF/XML release. To pass this principle, which is mandatory for our January 1^st 2024 deadline (see above), your primary ontology release MUST be in RDF/XML.

Figure 2. The four “layers” of interoperability in the OBO Foundry.

Spotlight on Software Tools

We continue spotlighting important software tools for the Open Biomedical Ontologies (OBO) Foundry community in this issue. These tools play a vital role in collaborative efforts, ensuring data integrity and facilitating the editing and validation of ontologies.

The table below provides an overview of several of these tools, some of which are used and actively developed by members of the OBO Foundry community.

Events

OBO Academy: Monarch Seminar Series (ongoing)

• Tutorial 2024/01/24: Curation with Synonyms Tutorial

  This tutorial will discuss best practices for assigning synonyms during ontology curation. The focus is on concrete examples and common issues when determining the proper scope for a synonym.

Don’t forget you can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Updates on past events

• Chris Mungall gave an OBO Academy presentation on a framework called Enhancing curation workflows with CurateGPT. The presentation provided an overview of CurateGPT’s capabilities, including searching, querying, completing, extracting from text, finding evidence, and editing. Chris discussed evaluations on using the tool for automating parts of ontology development, such as defining terms and predicting relationships. The idea is for an integrated system to organize complex ontology curation workflows with collaboration with humans and AI.
• Chris Mungall and Nico Matentzoglu gave an introduction to OBO ontologies and related issues to the Pharma community as part of the Seminar Series “Demystifying Ontologies for Life Science Leaders”. The slides can be accessed here, the recording here.
• Nico Matentzoglu and Charles Tapley Hoyt gave their International Society for Biocuration Career award talks about “Closing the gap between effective biocuration and meaningful ontology development” and “Democratizing Biocuration”.
• Deepak R. Unni gave a presentation on principles and practices for open and reusable ontologies at a FAIR IMPACT Workshop on Governance of Semantic artifacts, and talked about ways that OBO Foundry actively facilitates interoperability. The Slides can be accessed here. The recording here.

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list (low-traffic, no spam)
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace (when you join the obo-discuss mailing list, the welcome message has an invitation link for the Slack workspace).
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are various roles in which you can contribute, including assisting with the production of this newsletter

One of our primary goals is to foster collaboration and celebrate the contributions of our community members. In this edition, we will shine a spotlight on some of our current members, highlighting their achievements and fostering a sense of connection and cooperation.

We encourage you to share your thoughts and ideas with the OBO Operations Committee, as your feedback helps shape the future of the OBO Foundry.

Thank you for being part of our community. We hope you enjoy this second edition and find it enriching and informative.

Best regards, The OBO Foundry Operations Committee.

In Memoriam: Remembering Michael Ashburner

We bid farewell to Michael Ashburner, a distinguished biologist and an unwavering advocate for open science. Ashburner, a pioneering figure in genetics, bioinformatics, and the OBO Foundry, passed away on July 10, 2023, at 81. His visionary leadership at EMBL-EBI left an indelible mark on bioinformatics. He sequenced the Drosophila genome, co-founding FlyBase and shaping ontologies like GO and ChEBI. Advocating for open science, he championed genome accessibility and open publishing. Honored with awards such as the Gregor Mendel Medal, his legacy inspires future scientists. Our heartfelt condolences go out to his family, friends, and colleagues.

The OBO Foundry Operations Committee.

Highlights

Passing the OBO Dashboard will become mandatory on January 1^st 2024

On January 1^st, 2024, OBO Foundry will add a visual indicator to the https://obofoundry.org/ home page ontology list that shows each ontology’s compliance state (compliant / noncompliant) with respect to the dashboard report provided at http://dashboard.obofoundry.org/dashboard/index.html. Non-compliant ontologies will be sorted to the bottom of their default ontology-by-topic view group, and shaded. This is a purely informative indicator to enable OBO users to be aware of certain quality and maintenance issues that may affect their reuse plans; as well, it encourages ontology curators to strive for greater quality control excellence. Some key points:

Only dashboard (black X on a red background) errors cause non-compliance. Warnings (yellow triangle) or information (blue i) in the final “Summary” column are ok.

An explanation of the dashboard report is available here (link to dashboard video).

The “Maintained” column is dedicated to indicating recent updates to content in the ontology, and has been changed to avoid an error state. A warning is shown for inactivity beyond 2 years; an information icon is provided for 1-2 year inactivity. Note that the OBO Maintenance principle also asks that each ontology keep up to date with scientific consensus about its content, but this is not evaluated in the dashboard.

Moving forward, we will provide some guidance on how to pass specific errors on the OBO Dashboard. In this issue, we will explain how to pass the “Open” principle. For details, see “Spotlight on OBO Principles”.

Decisions Made and Important Updates

• All terms in New Ontology Requests MUST follow the OBO identifier scheme (often they are accidentally written wrongly, e.g. using https instead of http). There MUST NOT be a term with the same meaning available in another OBO Foundry ontology, ie there must not be a term referring to a concept that already exists in another OBO Foundry ontology (whether or not the label is identical). There SHOULD NOT be another OBO Foundry ontology whose scope covers any of the new terms. See Standard Operating Procedures.
• NCIT does NOT count when term overlap with other ontologies is determined. This is relevant because new ontologies are not allowed to create new terms for concepts that already exist in OBO. See meeting of 27th June 2023.
• Ontologies which redirect to OLS are now redirecting to OLS4.

Ongoing Discussions

Here, we list some of the more important discussions happening around the OBO-sphere:

• The OBO community discusses the best approach to managing COB identifiers (IDs) and mappings. The discussion revolves around the question of whether COB should mint new identifiers in the COB namespace, or re-use identifiers from existing OBO ontologies. Both have advantages and disadvantages. Join the discussion.
• This year, we have frequently stumbled across the question of whether an OBO ontology needs to be somehow related to the Biomedical or Biological domain or not. Give us your opinion!

Ontologies

In this edition of the OBO newsletter, we will explore aspects of the procedure for requesting the inclusion of a new ontology in the OBO Foundry. Today, we will talk about clearly defining the ontology’s purpose and scope.

Clearly define the ontology’s purpose and scope.

Clearly defining the purpose and scope of the ontology is a crucial step when submitting a new ontology to the OBO Foundry. This should include the ontology’s goals, intended applications, and the domain it covers. By articulating the purpose, developers highlight the objectives and benefits for the scientific community, along with potential use cases. Defining the scope entails specifying the aspects of the domain that the ontology will address and what it won’t cover while considering the appropriate level of detail. This information enables reviewers to assess the ontology’s relevance, significance, and potential impact, ensuring alignment with the OBO Foundry’s goals. A well-defined purpose and scope increase the chances of acceptance and integration into the suite of OBO Foundry ontologies.

New Ontology requests

• The Occupation Ontology (OccO) was recently submitted for inclusion in the OBO Foundry ontologies. The OccO developers actively communicate with OBO Foundry operations members to ensure the ontology adheres to OBO Foundry principles. OccO provides an initial ontological representation of occupational information from the United States Department of Labor’s Standard Occupational Classification (SOC) system, as enhanced by the ONet system. These occupational taxonomies are developed through a collaboration between the Department of Labor, Bureau of Labor Statistics, and the ONet Program - the primary source of occupational data in the United States. In line with OBO Foundry guidelines, OccO reflects the 2019 ONet-SOC taxonomy based on the 2018 SOC. The underlying ONet data is provided by the U.S. Department of Labor Employment and Training Administration (USDOL/EGA).

Spotlight on Ontologies

In this issue, we would like to highlight three ontologies from the OBO Foundry family: the Human Phenotype Ontology (HPO), the Cell Ontology (CL), and the Ontology for Biomedical Investigations (OBI).

• Ontology for Biomedical Investigations (OBI) provides a comprehensive framework for describing biological and clinical investigations. It encompasses various aspects of biomedical research, such as assays (covering all aspects of data generation), material processing, devices, protocols, data, and analysis methods. The latest OBI release includes over 4,000 terms, and re-uses key terms and relationships from other OBO ontologies wherever possible to connect aspects of an investigation to the biomedical terms in other OBO ontologies. OBI was founded in 2006 as a merger of several previous efforts focusing on specific individual experimental techniques (e.g. genomics, proteomics). OBI development has been driven by the specific needs of individual projects, and thus provides more detailed coverage in areas relevant to those projects. OBI continuously seeks input and contributions to broaden this coverage, and welcomes new members to join the active and open weekly development calls.
• Human Phenotype Ontology (HPO) is an ontology developed by the Monarch Initiative used to describe human phenotypic abnormalities seen in genetic disorders and clinical research. It provides a structured representation of abnormal characteristics associated with diseases. HPO helps researchers and clinicians share and integrate phenotypic data, making understanding and diagnosing genetic disorders easier. It uses a hierarchical organization and semantic relationships between terms and allows for annotation of genes and diseases. HPO is used in multiple diagnosis and variant prioritization tools, aiding healthcare professionals and researchers in identifying and classifying genetic conditions. Recently, HPO has released an international edition which covers different languages such as Chinese, Turkish, Japanese, Spanish and Czech (https://obophenotype.github.io/hpo-translations/). The translations are displayed in the HPO browser (e.g. https://hpo.jax.org/app/browse/term/HP:0001166) and OLS (https://www.ebi.ac.uk/ols4/ontologies/hp).
• Cell Ontology (CL) is an ontology designed to classify and describe cell types across different organisms. It serves as a resource for model organism and bioinformatics databases. The ontology covers a broad range of cell types in animal cells, with over 2700 cell type classes, and provides high-level cell type classes as mapping points for cell type classes in ontologies representing other species, such as the Plant Ontology or Drosophila Anatomy Ontology. Integration with other ontologies such as Uberon, GO, CHEBI, PR, and PATO enables linking cell types to anatomical structures, biological processes, and other relevant concepts. The Cell Ontology was created in 2004 and has been a core OBO Foundry ontology since the start of the Foundry. Since then, CL has been adopted by various efforts, including the HuBMAP project, Human Cell Atlas (HCA), cellxgene platform, Single Cell Expression Atlas, BRAIN Initiative Cell Census Network (BICCN), ArrayExpress, The Cell Image Library, ENCODE, and FANTOM5, for annotating cell types and facilitating cellular reference mapping, as documented through various publications and examples.

Members and Volunteers

Member Spotlight:

We are delighted to feature two OBO Foundry members in this month’s spotlight! Let us introduce you to Darren Natale and Chris Stoeckert, both of whom have made outstanding contributions to our community.

Darren Natale

A member of the faculty at Georgetown University Medical Center (Washington, DC, USA) and the Protein Information Resource (headed by Dr. Cathy Wu) since 2002, Darren Natale obtained his PhD in Biology at the University of Buffalo (NY, USA) in 1993. A molecular biologist by training (specializing in the field of DNA replication), Darren began his foray into bioinformatics when he joined the then-recently-established COG protein classification project at NCBI as a curator in 1999. In 2002 he brought his classification expertise to GUMC/PIR for the then-new UniProt project. In 2006 he became interested in working with ontologies, and shortly thereafter joined the OBO Foundry. He is the manager of the Protein Ontology project, which provides an ontological representation of protein-related entities (principally, post-translationally modified proteoforms). Currently, his collaborations include the aforementioned UniProt and PRO, and the Pathways2GO project. He also leads a collaborative project designed to make IEDB epitope data widely available in UniProtKB, PRO, and iPTMnet. Along with participating in the development of several other ontologies, his principal contribution to the OBO Foundry is as an inaugural member of the OBO Foundry Operations Committee, and as long-time chair of the Editorial Working Group. His favorite aspects of working with the OBO Foundry community are the collaborative way challenges to ontological modeling are met, and the often spirited but always informative discussions.

Chris Stoeckert

Before retiring at the end of 2022, Chris Stoeckert, Ph.D., was a Research Professor of Genetics at the Institute of Biomedical Informatics at the University of Pennsylvania; he is now an adjunct professor at Penn. Originally a biophysicist and then a molecular and cell biologist, he spent most of his career working on databases supporting the mining of complex datasets. These have included databases on gene expression, orthologous proteins, pancreatic development, Alzheimer’s Disease genomics, and multiple resources associated with the NIAID VEuPathDB Bioinformatic Research Center supporting research on eukaryotic pathogens (e.g., PlasmoDB) and vectors. The database work led to involvement in the development of data standards such as MIAME (Minimal Information About a Microarray Experiment), MAGE-TAB format standard for reporting microarray experiments, and the development of biomedical ontologies such as the MGED Ontology. Chris is a founder and developer of the Ontology for Biomedical Investigations (OBI), has led the development of the Ontology for Biobanking (OBIB), and contributed to a variety of ontologies in the OBO Foundry. Most recently, he applied ontologies for integration and harmonization of clinical data using semantic graphs in the TURBO (Transforming & Unifying Research with Biomedical Ontologies) project at Penn. He has served on the OBO Foundry Operations Committee and participated in the Editorial Working Group. Chris has enjoyed watching the OBO Foundry grow from its beginnings and is excited about its future with the influx of new members and technology.

Spotlight on OBO Principles

The OBO Foundry has developed a series of principles that represent best practices for usable, sustainable, interoperable ontologies and serve as criteria for evaluating the potential inclusion of new ontologies. In this newsletter, we will discuss each of these principles, starting with Principle 1 in this issue.

“The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration” is the publication that lays the groundwork for the OBO Foundry’s principles. It focuses on the collaborative development of ontologies to enhance biomedical data integration. This paper discusses how the OBO Foundry plays an important role in facilitating a unified approach to managing biomedical information by establishing a framework for consistent and interoperable ontologies.

Principle: Open (principle 1):

OBO Foundry Principle 1 emphasizes open access of ontologies in the biological and biomedical domains. It mandates free availability for all users, with only origin acknowledgment and alteration constraints. The aim is to establish OBO Foundry ontologies as shared resources, benefiting the wider community. This principle aligns with fostering interoperable ontologies and encourages term reuse. The principle description outlines recommendations for ontology providers and re-users, establishing responsible sharing and usage practices. This principle sets a strong foundation for collaborative growth and knowledge exchange in biology and biomedicine.

How to Pass Open Principle on the OBO Dashboard

The Open Principle can be violated by missing an open license or when the ontology license differs from the one registered in the OBO Foundry. An OBO Foundry ontology must have either an equivalent or less restrictive license than Creative Commons Attribution 3.0 Unported (CC BY 3.0). More information on the license type can be found in the Recommendations and Requirements section on the principle description page. To resolve this problem, you must include the corresponding axiom based on the ontology serialisation used.

For an ontology serialized in RDF/XML:

<dcterms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>

For an ontology serialized in OBO:

property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/

The use of the annotation property http://purl.org/dc/terms/license is mandatory. For more information on the dashboard and passing the principles, refer to this YouTube video.

It is essential to use the same license to ensure consistency and clarity within the ontology and its representation in the OBO Foundry registry. This approach ensures that users and contributors can easily comprehend and follow the ontology’s usage and distribution terms and conditions. Kindly create an issue on GitHub to update it in the OBO Foundry registry.

Spotlight on Software Tools

Starting from this issue, we spotlight essential software tools that form the foundation of the Open Biomedical Ontologies (OBO) Foundry community. These tools play a central role in facilitating collaboration, upholding data integrity, and editing and validating ontologies. The table below lists some of the tools that are frequently used by (and, in some cases, developed by) members of the OBO Foundry community.

Events

International Society for Biocuration Annual General Meeting: 18 October 2023, 8-9:30am PT

The International Society for Biocuration will host their Annual General Meeting to update community members on happenings in the Society over the past year. This webinar will include talks by the 2023 Excellence in Biocuration Award Winners, Charles Tapley Hoyt, Laboratory of Systems Pharmacology Harvard Medical School, MA, USA, winner of the Early Career Award (talk abstract is here) and Nicolas Matentzoglu, Monarch Initiative, Semanticly, Greece, winner of the Advanced Career Award (talk abstract is here). More information about their awards is available here: https://www.biocuration.org/announcement-for-2023-winners-of-excellence-in-biocuration-awards/. To join the webinar, please fill out this registration form.

OBO Academy: Monarch Seminar Series (ongoing)

Monarch OBO Training is a virtual training session that is offered biweekly on Tuesdays at 9 am PT/12 pm ET; it provides semantic engineering training targeted towards members of the Monarch Initiative and OBO community (all are welcome to participate). The sessions focus on various relevant topics which are outlined here: https://oboacademy.github.io/obook/courses/monarch-obo-training/#schedule.

Recent Monarch Training topics have included:

• How to determine if two entities are the same?
• Modern prefix management with Bioregistry and curies, led by Charlie Hoyt

Don’t forget you can vote for future training topics here: https://github.com/OBOAcademy/obook/discussions/categories/tutorial-requests

Updates on past events

• The OBO Technical Working group presented various OBO tools and practices at the Ontology Summit 2023. The Ontology Summit 2023 recordings are available in the Ontology Summit YouTube Channel.
• The OBO Academy team presented the OBO Training at ICBO 2023 this year.
  • Info: https://oboacademy.github.io/obook/courses/icbo2023/
  • Recording: Part 1, Part 2

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list (low-traffic, no spam)
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace (when you join the obo-discuss mailing list, the welcome message has an invitation link for the Slack workspace).
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are various roles in which you can contribute, including assisting with the production of this newsletter.

In this issue, you will find a range of content, including general announcements, training opportunities, and details about recent and upcoming events. Our goal with the OBO Foundry’s Quarterly Newsletter is to inform community members about the latest activities and advancements within the OBO Foundry.

Here we’ll announce the addition of new members to our community, praising their contributions and expertise. In future issues, we will shine a spotlight on some of our current members, fostering a sense of connection and cooperation.

Your input and suggestions are highly valued, and we eagerly invite you to share your thoughts and ideas. Please get in touch with the OBO Operations Committee anytime!

Thank you for reading, and we hope you enjoy the inaugural edition of the OBO Foundry Newsletter.

Best regards, The OBO Foundry Operations Committee.

Highlights

The OBO Foundry celebrates its 20-year anniversary

The OBO Foundry, established in 2003, is an international collaborative effort dedicated to developing and promoting high-quality, interoperable ontologies for biology, biomedicine, and related domains. Guided by principles of openness, collaboration, and best practices, the OBO Foundry has played a crucial role in advancing the field of biomedicine. By fostering the creation of ontologies that facilitate data exchange, knowledge discovery, and cooperation, the initiative has significantly contributed to the standardization and integration of ontologies. Its impact is evident in the broad adoption and utilization of its ontologies, which have become indispensable tools in biomedical research and applications. The OBO Foundry has attracted a diverse community of researchers, developers, and users from various biological and biomedical disciplines, reinforcing its mission of advancing data integration and analysis in research and clinical practice.

Ontologies

In this inaugural edition of the OBO newsletter, we want to remind you of the procedure for requesting the inclusion of a new ontology in the OBO Foundry:

1. Clearly define the ontology’s purpose and scope.
2. Review OBO Foundry Principles for alignment.
3. Check existing ontologies to avoid duplication.
4. Contact the OBO Foundry community to express interest and seek feedback.
5. Develop the ontology based on discussions and best practices.
6. Submit the ontology for review and feedback.
7. If accepted, add to the website and ensure ongoing maintenance. For detailed instructions, refer to the official documentation or engage with the OBO Foundry community.

We evaluate new ontologies for possible inclusion in the OBO Foundry on an ongoing basis. These carefully reviewed and curated ontologies cover different biomedical domains, enhancing data integration and collaboration within the community.

The list of topics for the 186 active ontologies accepted by the OBO community as of 2023 include agriculture, anatomy and development, biological systems, chemistry and biochemistry, diet, metabolomics, and nutrition, environment, health, information, information technology, investigations, microbiology, organisms, phenotype, and simulation. These diverse topics highlight the broad scope of ontologies developed and accepted by the OBO community, contributing to improvements in data integration and knowledge discovery in the biomedical domain.

Recently accepted ontologies include:

• Alzheimer’s Disease Ontology
• Next Generation Biobanking Ontology
• Vertebrate Breed Ontology

Spotlight on Ontologies

In every newsletter, we would like to highlight one or two ontologies from the OBO Foundry family to promote their use. Today, we introduce the Core Ontology for Biology and Biomedicine (COB) and the OBO Metadata Ontology (OMO), two ontologies fundamental to the vision of OBO interoperability.

• Core Ontology for Biology and Biomedicine (COB): An upper level ontology for the domain of Biology and Biomedicine. The OBO community has produced a large number of ontologies that cover biological and biomedical entities from anatomy, chemistry, assays and chemicals to diseases and phenotypes. While many ontologies have aligned with the Basic Formal Ontology (BFO), we have been lacking an easy to understand top-level that can be used by domain experts. The goal of COB is to organize the core types of biological entities into a small top level ontology, serving as an upper layer for biological data integration and querying. Establishing a basic community-wide agreement on the semantics of these core entities is a difficult task, but central for a core vision of OBO: decentralized development of interoperable ontologies. To contribute to the discussion, use the COB issue tracker.
• OBO Metadata Ontology (OMO): The OBO Metadata Ontology (OMO) defines all the standard properties used by OBO ontologies for both on ontology and term level. The goal of OMO is complementary to that of COB: to ensure that OBO wide, people that need to annotate metadata such as synonyms, contributors, term tracker items and ontology licenses do so using the exact same property, thereby facilitating interoperability. OMO is governed by the community consensus, which means that anyone can suggest changes and editions and put them to a vote. To propose new properties for inclusion, please use the OMO issue tracker.

Members and Volunteers

Our vibrant community of OBO Foundry members and volunteers is the driving force behind our success. Comprising professionals from different fields, they contribute their time and expertise to develop and assess high-quality ontologies and advance principles and best practices for interoperable ontologies. Their collaborative efforts support data integration, knowledge discovery, and interdisciplinary collaboration.

OBO is led by a volunteer team consisting of ontology maintainers and stakeholders (the ‘OBO operations committee’). This team performs multiple duties, including maintaining the site, stewarding the principles, and curating ontology metadata. The committee is divided into various subgroups which are concerned with the following problems:

• The Technical Working Group is involved in maintaining the technical infrastructure for the OBO Foundry. This includes establishment of policies to be implemented in common tools, website maintenance, calls, etc.
• The Editorial Working Group is involved in reviewing OBO Foundry ontologies and setting policies. Primary tasks are to conduct reviews, as well as all activities that enable that process, such as tool building for automated validation, website maintenance of the review results, or leading calls and taking notes.
• The OBO Foundry Outreach Working Group is involved in public relations for the OBO Foundry. This includes monitoring and following up discussions on mailing lists, preparing documentation and educational materials, and presenting OBO Foundry activities at workshops, conferences, or other venues.
• The OBO Academy is a community run education resource concerned with documenting many best practices that go beyond OBO Principles, and provide extensive training materials for all the technology developed and supported by the technical working group.

Recently, the OBO Operations Committee introduced a more refined role system in the OBO Foundry which clearly documents the work that needs to be performed on an ongoing basis. The new roles and their responsibilities are listed on the website.

By collaborating across these different areas and pulling together volunteers from a wide range of expertise, the OBO operations committee actively supports the vision of the OBO Foundry. The Standard Operating Procedure to become a member of the committee (still in development) is documented here. Reach out on Slack (obo-community channel) or via our obo-discuss mailing list if you are interested in joining.

New Volunteers

In this section we introduce the volunteers that recently joined the OBO Operations Committee. Mathias Brochhausen recently rejoined the OBO Operations Committee, after a period of absence. Welcome back Mathias!

Picture	Name	GitHub	Affiliation	Country	Role
	Anita R. Caron	anitacaron	European Bioinformatics Institute (EMBL-EBI), Cambridge	UK	OBO Dashboard Maintainer
	Deepak R. Unni	deepakunni3	SIB Swiss Institute of Bioinformatics, Basel	Switzerland	Registry Metadata Steward
	Erik Whiting	erik-whiting	University of Nebraska, Lincoln, NE	USA	OBO Website Coordinator
	Leila Kiani	LK112019	National Institutes of Health (NIH)	USA	OBO Newsletter Steward
	Paul Fabry	pfabry	Université de Sherbrooke, Québec	Canada	OBO New Ontology Request (NOR) Manager
	Ray Stefancsik	rays22	European Bioinformatics Institute (EMBL-EBI), Cambridge	UK	Technical Working Group OBO Operations liaison

Decisions Made and Important Updates

Decisions regarding changes to OBO principles

OBO Foundry publishes a set of principles that capture ontology best practices and that are used to assess new ontologies that wish to be included. We continuously review, refine, and clarify our principles to ensure that they support our commitment to ontological excellence. Below are some recent updates.

• NEW Principle 13 (Notification): Announcing major changes to stakeholders ahead of release. Principle 13 of the OBO Foundry emphasizes the importance of announcing significant changes to relevant stakeholders and collaborators before the ontology’s release. This proactive notification allows stakeholders to provide input on upcoming changes and update any dependencies affected by those changes.
• NEW Recommendation that ontology developers include guidelines and instructions for making contributions to ontology terms and discussions. Text to this effect has been added to Principle 8 (Documentation), Principle 10 (Commitment to Collaboration), and Principle 20 (Responsiveness).
• NEW Table of Contents added to principles pages. This is to aid users in finding information of interest.
• CLARIFICATION The OBO Foundry has made explicit the (previously implied) requirement for English language definitions (Principle 6). This was done both for pragmatic reasons (e.g., to enable reviews of new ontologies), and to match the similar requirement for English language labels and other fields (Principle 12). Discussions on how best to use/specify other languages is ongoing.

Updates from the technical working group

• On the 3rd June, we provisionally activated https support for our ontology PURLs. This means that from now on, you can access OMO not only through http://purl.obolibrary.org/obo/omo.owl, but also https://purl.obolibrary.org/obo/omo.owl! Follow the discussion here. Note that this does not extend to the use of term identifiers. While this identifier now resolves: https://purl.obolibrary.org/obo/OMO_0002000, you MUST NOT use https IRIs in your ontology, because https://purl.obolibrary.org/obo/OMO_0002000 and http://purl.obolibrary.org/obo/OMO_0002000 are fundamentally different things on RDF level.
• New versions of ROBOT (1.9.4) and the Ontology Development Kit (ODK, 1.4.1) were made available on the 23rd May 2023. ROBOT and ODK are two tools extensively supported by the OBO Technical Working Group.

Ongoing Discussions

Here, we list some of the more important discussions happening around the OBO-sphere:

• The definition of a “disease” class in COB is, not surprisingly, one of the hardest problems to get agreement on. The discussion has stalled, and needs to be re-invigorated.
• What should happen on 01.01.2024 when passing the Dashboard becomes mandatory? Get involved in the discussion!
• Some of us would like to visually separate permanently defective (e.g. unparseable, inconsistent) ontologies from the rest. Join the discussion.
• We are discussing the Standard Operating Procedure for activating a new OBO Principle!
• We are discussing the introduction of a new ontology status, unresponsive, for ontologies that do not respond to any of the regular communication channels.

New Version of Protégé is now available

Protégé is a popular open source ontology editor used by many ontology developers within and beyond the OBO Foundry. A new release of Protégé 5.6.2 is now available. You can download it from: https://github.com/protegeproject/protege-distribution/releases/tag/protege-5.6.2. Note that it is recommended that all OBO Foundry ontology editors use this latest version of Protégé for editing.

This version primarily addresses a bug affecting macOS users who could not save files due to the absence of the file-saving dialog (ticket #1106).

Rest assured, the new release maintains compatibility with the OWL API 4.5.25, ensuring a seamless upgrade without any serialization issues. The Protege developers appreciate your feedback to help identify bugs, which allows improvements to Protege for all users. Bugs and feature requests can be reported here: https://github.com/protegeproject/protege/issues or via the Protege Slack channel in the OBO Foundry workspace.

Protege is now developed under a community contribution model. Much gratitude goes to Damien Goutte-Gattat and Huseyin Kir for their work to help deliver this new release and implement these fixes.

Updates around OBO Academy

The OBO Academy is an educational initiative that supports ontology users and developers in the OBO community. It offers freely available, online, self-paced training and educational resources to enhance ontology literacy and foster collaboration. With a focus on knowledge sharing and community engagement, the OBO Academy invites participation and contributions to enrich its educational offerings. All of the content is available in a GitHub repository and anyone is welcome to make pull requests to suggest new content or edit existing content. Please join the conversation on the OBO Academy Slack channel.

Promotion of OBO Academy Materials

The National Student Data Corps, an initiative within the Northeast Big Data Innovation Hub, focuses on leveraging data for societal challenges. They offer big data training materials, freely available at https://nebigdatahub.org/nsdc/. A new collaboration was recently formed between Florence Hudson from Columbia University and the OBO Academy team, and OBO Academy resources will be shared on this site, as well as on Columbia University’s COVID Info Commons site.

International Society for Biocuration Career Awards

The International Society of Biocuration (ISB) has recently announced the winners for the prestigious Early Career Award, Advanced Career Award, and Lifetime Achievement Award. We are delighted to announce that two of the winners of this year’s “Excellence in Biocuration Award” are active contributors to the OBO Foundry: The Early Career Award was given to Charlie Hoyt, and the Advanced Career Award was given to Nico Matentzoglu.

Charles Tapley Hoyt, a Research Fellow at Harvard Medical School, is an exceptional biocurator. He leads the development of community datasets and databases like the Bioregistry, Biomappings, and Chemical Roles Graph. He actively contributes to the OBO Foundry ontology community and related standards development, including the SSSOM standard. Charlie’s active engagement in the Biocuration community includes co-chairing the recent Biocuration 2023 conference.

Nicolas Matentzoglu, a celebrated figure in bio-ontology and biocuration, passionately advocates open science. He co-leads the OBO Academy and leads the development of the Ontology Development Kit (ODK). Nico also spearheads the development of the Simple Standard for Sharing Ontological Mappings (SSSOM). His efforts have attracted and united diverse contributors in the biocuration community.

We congratulate Charlie and Nico on their well-deserved awards!

Events

OBO Academy: Monarch Seminar Series (ongoing)

Monarch OBO Training is a virtual training session that is offered biweekly on Tuesdays at 9 am PT/12 pm ET; it provides semantic engineering training targeted towards members of the Monarch Initiative and OBO community (all are welcome to participate). The sessions focus on various relevant topics which are outlined here: https://oboacademy.github.io/obook/courses/monarch-obo-training/#schedule. Recent sessions focused on using ChatGPT in ontology workflows and modeling with taxon constraints. Videos of past events are available online. Join the obo-academy channel in the OBO slack to learn more.

ICBO OBO Tutorial 2023: Using and Reusing Ontologies

Date: Exact date TBD. Workshops/tutorials will be held August 28-30, 2023
Location: In person at ICBO2023 in Brazil and virtual
Organizers: Nicole Vasilevsky and Nico Matentzoglu
The ICBO OBO Tutorial 2023, “Using and Reusing Ontologies,” is targeted towards novice and experienced ontology users and developers. The tutorial, a longstanding tradition at ICBO, introduces OBO and ontologies in general and will include more advanced topics including using ROBOT and ChatGPT.

Workshop on Ontologies for Infectious and Immune-mediated Disease Data Science (OIIDDS)

Announcing the first workshop on Ontologies for Infectious and Immune-mediated Disease Data Science (OIIDDS). As part of ICBO 2023 workshops & Tutorials, this interactive event at Brasilia University in Brazil brings together experts in ontologies, data science, infectious disease, and immunology. We invite researchers to submit their work on ontologies, knowledge graphs, and applications. Find more details on submission guidelines here. Take advantage of this opportunity to explore cutting-edge developments in this field.

Ways to be part of the OBO Foundry community

There are many ways to be part of the OBO Foundry community, beyond using our website to find ontologies of interest. For example:

• Join the obo-discuss mailing list (low-traffic, no spam)
• If you are interested in the technical aspects, you can also join the obo-tools mailing list
• Join the conversation in our Slack workspace
• Use our public issue tracker to report a problem you discovered on obofoundry.org or request a new feature
  • Note that most issues relating to individual ontologies (e.g., a request to add a new term) should be added to the issue tracker for the specific ontology
• Propose a fix to an issue you see on our issue tracker (this is done via a GitHub Pull Request, which will be checked and approved by someone in the Foundry). Since all of our code is publicly readable, you may be able to pinpoint where a bug fix needs to go.
• Request that your ontology be considered for inclusion in the Foundry
• If you want to take your contributions to OBO Foundry to the next level, you can nominate yourself to be considered for the OBO Operations Committee. There are various roles in which you can contribute, including assisting with the production of this newsletter.