Papers that cite the OBO Foundry

Antezana E, Tsiporkova E, Mironov V, et al. 2006 "A cell-cycle knowledge integration framework", Lecture Notes in Computer Science 4075: 19-34. http://www.psb.ugent.be/cbd/cco/cellcycleframework.pdf

Aranguren ME, Bechoffer S, Lord P, Sattler U, Stevens R 2007 "Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL", BMC Bioinformatics, 8: 57. http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1819394&blobtype=pdf

Arnaiz O, Cain S, Cohen J, Sperling L 2006 "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data", Nucleic Acids Res Dec 7. http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D439

Baker CJO, Shaban-Nejad A, Su X, Haarslev V, Butler G 2006 "Semantic Web infrastructure for fungal enzyme biotechnologists", J Web Semantics 4 (3). http://users.encs.concordia.ca/~haarslev/publications/JWS-2006.pdf

Bard JBL 2005 "Anatomics: the intersection of anatomy and bioinformatics", Journal of Anatomy 206 (1): 1-16 Jan. http://www.blackwell-synergy.com/doi/pdf/10.1111/j.0021-8782.2005.00376.x?cookieSet=1

Bittner T, Goldberg LJ 2006 "The Qualitative and Time-Dependent Character of Spatial Relations in Biomedical Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, 47-55. http://www.acsu.buffalo.edu/~bittner3/BittnerGoldbergKRMed.pdf

Blake JA, Bult CJ 2006 "Beyond the data deluge: Data integration and bio-ontologies", Journal of Biomedical Informatics 39 (3): 314-320. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16564748

Bodenreider O. 2006 "Lexical, terminological and ontological resources for biological text mining", in Ananiadou S, McNaught J, (eds.) Text mining for biology and biomedicine, Artech House, 43-66. http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006007.pdf

Bontas EP, Schlangen D, Schrader T 2005 "Creating ontologies for content representation - The OntoSeed suite", Lecture Notes in Computer Science 3761: 1296-1313. http://userpage.fu-berlin.de/~paslaru/papers/jods2006.pdf

Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H Kelso J. 2006 "A top-level ontology of functions and its application in the Open Biomedical Ontologies", Bioinformatics, Vol. 22 no. 14: e66-e73. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e66

Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA 2006 "The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case", BMC Bioinformatics 25 (7): 267. http://www.biomedcentral.com/1471-2105/7/267/abstract

Ceusters W 2006 "Towards a Realism-Based Metric for Quality Assurance in Ontology Matching", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Edited by Brandon Bennett, Christiane Fellbaum, New York: IOS Press, 321-332. http://ontology.buffalo.edu/bfo/Ontology_Matching.pdf

Ceusters W, Smith B 2006 "A Realism-Based Approach to the Evolution of Biomedical Ontologies", Proceedings of the Annual AMIA Symposium, Washington DC, 121-125. http://ontology.buffalo.edu/bfo/Versioning.pdf

Dameron O, Roques E, Rubin DL, Marquet G, and Burgun A 2006 "Grading lung tumors using OWL-DL based reasoning", In 9th International Protégé Conference. http://www.med.univ-rennes1.fr/~dameron/publis/2006protege-dameron.pdf

Dolbey A, Ellsworth M, Scheffczyk J 2006 "BioFrameNet: A Domain-Specific FrameNet Extension with Links to Biomedical Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, 87-94. http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-222/krmed2006-p10.pdf

Donnelly M, Bittner T, Rosse C 2006 "A formal theory for spatial representation and reasoning in biomedical ontologies", Artificial Intelligence in Medicine 36 (1): 1-27. http://www.acsu.buffalo.edu/~md63/DonnellyAIMed05.pdf

Friedberg I 2006 "Automated protein function prediction - the genomic challenge", Briefings in Bioinformatics 7 (3): 225-242. http://bib.oxfordjournals.org/cgi/content/abstract/bbl004?ijkey=n3AzMhAJ4nZjzAy&keytype=ref

Friedman C, Borlawsky T, Shagina L, et al. 2006 "Bio-Ontology and text: bridging the modeling gap", Bioinformatics 22 (19): 2421-2429. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2421

Fung KW, et al. 2005 "Integrating SNOMED CT into the UMLS: An Exploration of Different Views of Synonymy and Quality of Editing", Am Med Inform Assoc. http://www.jamia.org/cgi/reprint/12/4/486.pdf

Gardner SP 2005 "Ontologies and semantic data integration", Drug Discovery Today, 10 (14): 1001-1007. http://64.233.179.104/scholar?hl=en&lr=&safe=off&q=cache:RXb5cPWct5IJ:www.biowisdom.co.uk/docs/DDT_Ontologies_and_Semantic_Integ\ ration.pdf+

Gkoutos, GV 2006 "Towards a phenotypic semantic web", Current Bioinformatics, 1 (2): 235-246. http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000002/art00010

Haendel, MA, Neuhaus, F, Osumi-Sutherland, DS, Mabee, PM, Mejino JLV, Mungall, CJ, and Smith, B 2007 "The Common Anatomy Reference Ontology", in: A Burger, et al. (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, New York, Springer. http://www.acsu.buffalo.edu/~fneuhaus/caropreprint.pdf

Hahn U, Schulz S, 2007 "Ontological Foundations for Biomedical Sciences", in Artificial Intelligence in Medicine, 39 (3): 179-82. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=17321117

Harris MA, Clark JI, Ireland A, et al./Gene Ontology Consortium. 2006 "The Gene Ontology (GO) project in 2006", Nucleic Acids Research 34: D322-D326 Sp. Iss. SI Jan1. http://nar.oxfordjournals.org/cgi/screenpdf/34/suppl_1/D322.pdf

Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, and Wittbrodt J 2005 "MEPD: a resource for medaka gene expression patterns", Bioinformatics 2005 21(14):3195-3197; doi:10.1093/bioinformatics/bti478 . http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/14/3195

Hsing, M., Cherkasov, A. 2006 "Integration of Biological Data with Semantic Networks", Current Bioinformatics, 1 (3): 273-290. http://colab.cim3.net/file/work/SICoP/2006-10-10/Hsing_CBIO.pdf

Ingenerf J., Linder R. 2006 "Ontological Principles Applied to Biomedical Vocabularies". http://www.imbi.uni-freiburg.de/medinf/fctc-2006/docs/in_final.pdf

Johansson I. 2006 "Bioinformatics and biological reality", Journal of Biomedical Informatics 39 (3): 274-287. http://hem.passagen.se/ijohansson/information4.PDF

Kosseim L, Reda Siblini, Christopher J.O. Baker and Sabine Bergler 2006 "Using Selectional Restrictions to Query an OWL Ontology", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Edited by Brandon Bennett, Christiane Fellbaum, New York: IOS Press, 360-371. http://users.encs.concordia.ca/~kosseim/Publications/fois2006.pdf

Louie B, Mork P, Martin-Sanchez F, et al. 2007 "Data integration and genomic medicine", Journal of Biomedical Informatics, 40 (1): 5-16. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-4JF8G2S-1&_user=681891&_coverDate=02%2F28%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000037419&_version=1&_urlVersion=0&_userid=681891&md5=79d8eb7d16f9905770ba994d169d1e8d

Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M 2007 "Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish", J Exp Zoolog B Mol Dev Evol. 2007 Sep 15;308(5):655-6.

Maglia AM, et al. 2007 "An anatomical ontology for amphibians", Pacific Symposium on Biocomputing, 12: 367-378. http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf

Malmstrom L, Marko-Varga G, Westergren-Thorsson G, et al. 2006 "2DDB - a bioinformatics solution for analysis of quantitative proteomics data", BMC Bioinformatics 7. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16549013

Masseroli M, Pinciroli F 2006 "Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: Three tool comparison", Computers in Biology and Medicine, 36 (7-8): 731-747. http://www.htscreening.org/showabstract.php?pmid=16165121

Morrison N, Cochrane G, Faruque N, et al. 2006 "Concept of sample in OMICS technology", Omics - A Journal of Integrative Biology 10 (2): 127-137. http://www.liebertonline.com/doi/pdfplus/10.1089/omi.2006.10.127

Myhre S, Tveit H, Mollestad T, et al. 2006 "Additional Gene Ontology structure for improved biological reasoning", Bioinformatics 22 (16): 2020-2027. http://bioinformatics.oxfordjournals.org/cgi/reprint/22/16/2020

DA Natale, CN Arighi, W Barker, J Blake, TC Chang, Z Hu, H Liu, B Smith, and CH Wu 2006 "Framework for a Protein Ontology", Proceedings of the 1st international workshop on Text mining in bioinformatics, Arlington, Virginia, 29-36. http://pir.georgetown.edu/pirwww/about/doc/tmbio19-natale.pdf

Neuhaus F, et al. "Modelling Principles and Methodologies: Relations in Anatomical Ontologies", in: A Burger et al. (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, New York: Springer, in press.

Okada M, Sugimoto Y, Yoshikawa S, et al. 2006 "Drug Interaction Ontology (DIO) and the resource-sensitive logical inferences", Lecture Notes in Computer Science; 4060: 616-642.

Paul S, et al. 2006 "A semantically enabled formalism for the knowledge management of Parkinson's disease". Medical Informatics and the Internet in Medicine. http://www.informaworld.com/smpp/content?content=10.1080/14639230500299220

Philippi S, Kohler J 2006 "Addressing the problems with life-science databases for traditional uses and systems biology", Nature Reviews Genetics 7 (6): 482-488. http://www.nature.com/nrg/journal/v7/n6/abs/nrg1872.html

Rogers JE 2006 "Quality assurance of medical ontologies", Methods of Information in Medicine 45 (3): 267-274. http://www.schattauer.de/index.php?id=1268&pii=me06030267&no_cache=1

Rosenbloom ST, Miller RA, Johnson KB, et al. 2006 "Interface terminologies: Facilitating direct entry of clinical data into electronic health record systems", Journal of the American Medical Informatics Association 13 (3): 277-288. http://www.jamia.org/cgi/reprint/13/3/277

Ruttenberg A, Clark T, et al. 2007 "Advancing translational research with the Semantic Web", BMC Bioinformatics, 8(Suppl 3):S2. http://www.biomedcentral.com/1471-2105/8/S3/S2

Ruttenberg A, Rees JA, Luciano JS 2005 "Experience using OWL DL for the exchange of biological pathway information", in OWL Experiences and Directions. http://www.mindswap.org/2005/OWLWorkshop/sub37.pdf

Ruttenberg A, Rees J, Zucker J. 2007 "What BioPAX communicates and how to extend OWL to help it", OWLED. http://www.webont.org/owled/2006/acceptedLong/submission_26.pdf

Schulz S, Elena Beisswanger, Udo Hahn, Joachim Wermter, Anand Kumar and Holger Stenzhorn 2006 "From GENIA to BIOTOP: Towards a Top-Level Ontology for Biology", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Ed. by B. Bennett, C. Fellbaum, New York: IOS Press, 103-114. http://www.ifomis.uni-saarland.de/people/holger/publications/fois06.pdf

Schulz S, Hanser S, Hahn U, et al. 2006 "The semantics of procedures and diseases in SNOMED CT", Methods of Information in Medicine 45 (4): 354-358. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&list_uids=16964349&cmd=Retrieve&indexed=google

Schulz S, Jansen L 2006 "Lmo-2 interacts with elf-2" On the Meaning of Common Statements in Biomedical Literature, O. Bodenreider, ed., Proceedings of KR-MED, 37-45.

Schulz S, Kumar A, Bittner T 2006 "Biomedical ontologies: What part-of is and isn't", Journal of Biomedical Informatics 39 (3): 350-361. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16442850&dopt=Citation

Schulz S., S. Hanser, U. Hahn, J. Rogers 2006 "The Semantics of Procedures and Diseases in SNOMED CT", Methods of Information in Medicine, 45/4. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&list_uids=16964349&cmd=Retrieve&indexed=google

Skusa A, Ruegg A, Kohler J 2005 "Extraction of biological interaction networks from scientific literature", Briefings in Bioinformatics 6 (3): 263-276. http://bib.oxfordjournals.org/cgi/reprint/6/3/263?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=skusa%2C+a&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT

Slaughter LA, et al. 2005 "Semantic representation of consumer questions and physician answers". Int J Med Inform. http://lhncbc.nlm.nih.gov/lhc/docs/published/2005/pub2005050.pdf

Smith B, Ashburner M, Rosse C, Bard C, Bug W, Ceusters W, Goldberg L J, Eilbeck K, Ireland A, Mungall C J, The OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann R H, Shah N, Whetzel P L and Lewis S (2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", Nature Biotechnology 25, 1251 - 1255. http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html

Soldatova LN, Clare A, Sparkes A, King RD 2006 "An ontology for a robot scientist", Bioinformatics 22 (14): e464–e471. http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e464

Sprague J, et al. 2006 "The Zebrafish Information Network: the zebrafish model organism database", Nucleic Acids Res. 34, D581-D585. http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D581

Strizh IG 2006 "Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study", Bioessays 28 (2): 199-210. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16435295&dopt=Abstract

Thomas CJ, Sheth AP, and York WS 2006 "Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Ed. by B. Bennett, C. Fellbaum, NY: IOS Press, 115-127. http://lsdis.cs.uga.edu/library/download/GlycO_FOIS_2006.pdf

van Gurp M, Decoene M, Holvoet M, Casella dos Santos M 2006 "LinKBase, a Philosophically-Inspired Ontology for NLP/NLU Applications", O. Bodenreider, ed., Proceedings of KR-MED, 67-75.

Vizenor L, Bodenreider O 2006 "Using dependence relations in MeSH as a framework for the analysis of disease information in Medline", Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006): 76-83. http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-177/paper_vizenor.pdf

Vizenor L, Bodenreider O, Peters L, McCray AT 2006 "Enhancing biomedical ontologies through alignment of semantic relationships: Exploratory approaches", Proc AMIA Annual Symp: 804-808. http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006059.pdf

Whetzel PL, et al. 2006 "The development of FuGO--An ontology for functional genomics experiments", Omics: A Journal of Integrative Biology, 10 (2), 199-204. http://www.liebertonline.com/doi/pdf/10.1089/omi.2006.10.199

Zhang S, Bodenreider O. 2006 "NLM anatomical ontology alignment system. Results of the 2006 ontology alignment contest", Proceedings of the Ontology Alignment Evaluation Initiative 2006 Campaign (OAEI):145-156. http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006061.pdf

Zhang S, Bodenreider O 2006 "Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy", Computers in Biology and Medicine 36 (7-8): 674-693. http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006023.pdf

Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, Zhou Z, Wei L 2006 "SynDB: a Synapse protein DataBase based on synapse ontology", Nucleic Acids Res, Nov 10. http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D737

Zhou L, Tao Y, Cimino JJ, et al. 2006 "Terminology model discovery using natural language processing and visualization techniques", Journal of Biomedical Informatics 39 (6): 626-636. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16360342