Publications

Publications of the OBI consortium and its members

 * Applied Ontology, 2011 6(1), 23-33 MIREOT: The minimum information to reference an external ontology term, Courtot, M., Gibson, F., Lister, A. L., Malone, J., Schober, D., Brinkman, R. R., & Ruttenberg, A.
 * Applied Ontology, 2011 6(1), 13-22. Overcoming the ontology enrichment bottleneck with Quick Term Templates, Rocca-Serra, P., Ruttenberg, A., O'Connor, M. J., Whetzel, P. L., Schober, D., Greenbaum, J., Mélanie Courtot, Ryan R. Brinkman, Susanna Assunta Sansone, Richard Scheuermann, The OBI Consortium, Peters, B.
 * J Biomed Semantics. 2010. Modeling biomedical experimental processes with OBI, Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jr., Jessica A Turner, Jie Zheng, and the OBI consortium
 * OWLED 2008. The OWL of Biomedical Investigations, Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Brinkman and Alan Ruttenberg.
 * Nat Biotechnol. 2007 Nov;25(11):1251-1255. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, The OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.
 * OMICS 2006;10(2):199-204. Development of FuGO: an ontology for functional genomics investigations. Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ, Taylor C, White J, Wood A. PMID: 16901226

Publications citing OBI

 * Structured Representation of Biomedical Experiments: A Bottom-Up Approach. Cartik R. Kothari and Mark D. Wilkinson. IKE'08.
 * The EXACT description of biomedical protocols Larisa N. Soldatova, Wayne Aubrey, Ross D. King, and Amanda Clare
 * Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments de Marco Ario
 * SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses Nobuhiko Tanaka,1 Kazunori Waki,1 Hideki Kaneda,2 Tomohiro Suzuki,2 Ikuko Yamada,2 Tamio Furuse,2 Kimio Kobayashi,2 Hiromi Motegi,3 Hideaki Toki,3 Maki Inoue,3 Osamu Minowa,3 Tetsuo Noda,3 Keizo Takao,4 Tsuyoshi Miyakawa,4 Aki Takahashi,5 Tsuyoshi Koide,5 Shigeharu Wakana,2 and Hiroshi Masuya
 * Issues in learning an ontology from text Christopher Brewster, Simon Jupp, Joanne Luciano, David Shotton, Robert D Stevens, and Ziqi Zhang
 * RDFScape: Semantic Web meets Systems Biology Andrea Splendiani
 * CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data Michael Waters, Stanley Stasiewicz, B. Alex Merrick, Kenneth Tomer, Pierre Bushel, Richard Paules, Nancy Stegman, Gerald Nehls, Kenneth J. Yost, C. Harris Johnson, Scott F. Gustafson, Sandhya Xirasagar, Nianqing Xiao, Cheng-Cheng Huang, Paul Boyer, Denny D. Chan, Qinyan Pan, Hui Gong, John Taylor, Danielle Choi, Asif Rashid, Ayazaddin Ahmed, Reese Howle, James Selkirk, Raymond Tennant, and Jennifer Fostel
 * OntoFox: web-based support for ontology reuse Zuoshuang Xiang, Mélanie Courtot, Ryan R Brinkman, Alan Ruttenberg, and Yongqun He

Projects using OBI

 * NIF NIF has recently worked on data transformation terms in OBI, has aligned itself with Eagle I and BRO with respect to all resource description terms such as services and databases, and has provided instruments to OBI. NIF is working on swapping out nlx temporary identifiers with OBI term identifiers to label data in the resource registry as well as search for both registry items and data.
 * Eagle I
 * BRO
 * IEDB
 * ITPPR The Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies (e.g., genotyped isolates of parasites, phenotypes of transgenic parasites) for EuPathDB and to provide terms for annotating bioinformatics web services available through Galaxy.
 * FGED - MGED Ontology The Functional Genomics Data (FGED) Society has incorporated the MGED Ontology (MO) into OBI for use in annotating functional genomics studies especially with the MAGE-TAB format.
 * ISA The ISA (Investigation/Study/Assay) infrastructure is a user-friendly multi-domain data capture and management suite that allows the searching of OBI for terms to use in data entry.
 * MIBBI The MIBBI (Minimum Information for Biological and Biomedical Investigations) project features a range of both community-sourced and integrated reporting guidelines that indicate the use of OBI as a source of controlled terms.
 * CogPO CogPO starts with IAO and is working to harmonize with OBI where possible.
 * EFO Application ontology for ArrayExpress uses OBI and IAO classes, particularly assays
 * VO The Vaccine Ontology (VO) uses OBI for vaccine investigations
 * '''The Oral Health and Disease Ontology (OHD) uses OBI as part of the representation of dental procedures and materials

Projects using OBI listed on Bioportal website: http://bioportal.bioontology.org/ontologies/1123

Projects using OBI (merged list)
Immune epitope database uses OBI the vocabulary and data models. NIF has recently worked on data transformation terms in OBI, has aligned itself with Eagle I and BRO with respect to all resource description terms such as services and databases, and has provided instruments to OBI. NIF is working on swapping out nlx temporary identifiers with OBI term identifiers to label data in the resource registry as well as search for both registry items and data. All of the Eagle I data is entered as instances of OBI classes. The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application ontology for indexing and querying, and this effort is being guided by discussions within the ontology community aimed at promoting interoperability. We will be inventorying laboratories, services, instruments, services, reagents, organisms, persons, protocols, human studies (metadata), tissue/biological sample repositories and training opportunities. The Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies (e.g., genotyped isolates of parasites, phenotypes of transgenic parasites) for EuPathDB and to provide terms for annotating bioinformatics web services available through Galaxy. The Functional Genomics Data (FGED) Society has incorporated the MGED Ontology (MO) into OBI for use in annotating functional genomics studies especially with the MAGE-TAB format. The ISA (Investigation/Study/Assay) infrastructure is a user-friendly multi-domain data capture and management suite that allows the searching of OBI for terms to use in data entry. The MIBBI (Minimum Information for Biological and Biomedical Investigations) project features a range of both community-sourced and integrated reporting guidelines that indicate the use of OBI as a source of controlled terms. CogPO starts with IAO and is working to harmonize with OBI where possible. Application ontology for ArrayExpress uses OBI and IAO classes, particularly assays. The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to develop a national infrastructure for managing, sharing, and analyzing a broad range of cardiac data. The EP Ontology will contain terms for describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques. The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO). NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing an integrated tool environment for storage and management of ERP data, ontologies, and ontology-based markup and analysis of data. A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts. The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI). The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. VO is a biomedical ontology in the domain of vaccine. VO uses OBI to represent vaccine investigations, for example, vaccine protection experiment.
 * IEDB
 * Neuroscience Information Framework
 * BRO
 * eagle-i
 * ITPPR
 * FGED - MGED Ontology
 * ISA
 * MIBBI
 * CogPO
 * EFO
 * Electrophysiology Ontology
 * Influenza Ontology
 * Neural ElectroMagnetic Ontologies
 * NCBO Annotator
 * NCBO Resource Index
 * An Ontology for Drug Discovery Investigations
 * Adverse Event Reporting Ontology
 * Vaccine Ontology (VO)