Find topic
General webs
Web tools
Help
|
Biomedical Ontologies Relevant to Mouse BIRN Data Management/Integration and Systems Interoperability
The following is a list of existing ontologies encapsulating the domains of biological knowledge under direct investigation in Mouse BIRN research projects. Some of these formal conceptual networks have existed for many years and are used ubiquitiously to provide a conceptual metadata framework in bio-molecular, medical and literature informatics. Others are still under development.
This list is meant to grow as both our use of these formalisms expands and new ontologies are added to the neuroinformatics armamentarium. Please feel free to provide suggestions and/or references to additional ontologies and ontological engineering applications relevant to managing distributed neuroinformatics systems to Dr. Maryann Martone or Bill Bug.
| Ontology |
Statusa |
As Of |
Structure¶ |
Reference |
| Neuronames† |
very active use for nearly a decade |
02 June 2005 |
|
Bowden DM, Dubach MF. (2003) NeuroNames 2002. Neuroinformatics. v1(1), p43-59. |
| Standard Nomenclature for Mus gross anatomy and development‡ |
in use at Edinburgh Mouse Atlas Project (EMAP) for several years |
02 June 2005 |
|
Baldock, R. A., Bard, J. B., Burger, A., Burton, N., Christiansen, J., Feng, G., Hill, B., Houghton, D., Kaufman, M., Rao, J., Sharpe, J., Ross, A., Stevenson, P., Venkataraman, S., Waterhouse, A., Yang, Y., Davidson, D. R.. (2003) EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics, v1, n5, p309-326. |
| Adult Mouse Anatomical Dictionary‡ |
in use at the Mouse Genome Informatics (MGI) site for several years. They have also integrated use of the EMAP developmental anatomy nomeclature cited above. |
02 June 2005 |
|
Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M. (2005) The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biology, v6, pR29, Feb 2005. |
| Brain Architecture Management System (BAMS) |
Curated knowledge map of neural architecture and connectivity in primates (human & macaque), felines (cat) and rodents (rat and mouse) |
02 June 2005 |
|
Bota M, Dong HW, Swanson LW. (2005) Brain Architecture Management System. Neuroinformatics. v3(1), p15-48. |
| Foundational Model of Anatomy (FMA) |
"...the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy." It is relavent to Mouse BIRN in that the curators of FMA are working with the National Cancer Institute’s consortium for Mouse Models of Human Cancer (MMHCC) to map equivalencies to mouse anatomy. |
02 June 2005 |
|
- Martin, R. F. and Mejino, J. L. V. and Bowden, D. M. and Brinkley, J. F. and Rosse, C. (2001) Foundational Model of Neuroanatomy: Implications for the Human Brain Project. Proceedings, AMIA Annual Fall Symposium, pages 438-442, Washington, DC.
- Travillian, R. S. and Rosse, C. and Shapiro, L. G. (2003) An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy. Proceedings, American Medical Informatics Association Fall Symposium, pages 669-673.
|
| The Genealogy Chart of Inbred Strains |
used heavily at Jackson Labs for over a decade; list codified 5 years ago; original list culled from terms in heavy use over a decade for annotation of the S.cerivisae, D.melanogaster and M.mus genome databases. |
02 June 2005 |
|
Beck JA, Lloyd S, Hafezparast M, Lennon-Pierce M, Eppig JT, Festing MF, Fisher EM.. (2000) Genealogies of mouse inbred strains.Nat Genet. Jan, v24(1), p23-5. |
| Mammalian Phenotype Browser‡ |
in use at JAX for a decade |
02 June 2005 |
|
Smith CL, Goldsmith CA, Eppig JT. (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.Genome Biol., v6, n1, pR7. |
| Mouse Ontology Resources from the Standards and Ontologies for Functional Genomics group‡ |
recent joint venture |
02 June 2005 |
|
focused on integrated formalisms for specifying mouse and human anatomy; hosts links to the following frameworks:
|
| SOFG Anatomy Entry List (SAEL)‡ |
newly derived from existing ontologies such as EMAGE, FMA, GALEN, GXD, MGED, etc. |
02 June 2005 |
|
-
-
Purpose- "The SAEL is an entry mechanism for computational access to anatomy resources, to facilitate automated information retrieval. It is a resource for curators, biologists, informaticians and developers of software supporting functional genomics."
Creation: "...was generated by EMAP, FMA, GALEN, GXD, MGED, EHDA under the auspices of SOFG and initial workshop funding by the MRC-HGU Edinburgh...currently maintained by the MGED ontology group with anatomical curation by Jackson Lab GXD database curator Terry Hayamizu.(content available as a web service). |
| Mouse Pathology Ontology‡ |
in use at Pathbase |
02 June 2005 |
|
Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Bjorn Rozel, Hannu Sariola, John P. Sundberg and Andrew Ward. (2005) Pathbase: a database of mutant mouse pathology. Nucleic Acids Research, v32, pD512-D515 (Database Issue). |
| The Gene Ontology (GO)‡ |
very active use for 5 years in bio-molecular & literature informatics |
02 June 2005 |
|
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. May, v25(1), p25-9. |
| The Cell Type Ontology‡ |
under development |
02 June 2005 |
|
Jonathan Bard, Seung Y Rhee and Michael Ashburner. (2005) An ontology for cell types. Genome Biology, v6, n2, pR21. |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) |
very mature; in use for over a decade in bio-molecular informatics |
02 June 2005 |
|
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. Jan 1, v32(Database issue), pD277-80. |
| Protein-Protein interactions from the Human Proteome Organizations (HUPO) Proteomics Standards Initiative (PSI)‡ |
? |
02 June 2005 |
|
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. (2004) The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. Feb, v22, n2, p177-83. |
| The Microarray Gene Expression Data (MGED) Ontology‡ |
in use for ~5 years |
02 June 2005 |
|
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J; Microarray Gene Expression Data (MGED) Society. (2002) Standards for microarray data.Science. Oct 18, v298(5593), p539. |
| Systematized Nomenclature of Medicine (SNOMED)† |
in active use in medical, literature & bio-molecular informatics for 40 years. |
02 June 2005 |
|
Kudla KM, Rallins MC. (1998) SNOMED: a controlled vocabulary for computer-based patient records. J AHIMA. May, v69(5), p40-4. |
| The Open Microscopy Environment (OME) ontology |
in use by users of OME for a few years |
02 June 2005 |
|
Ilya G Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager,
Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen,
Peter K Sorger and Jason R Swedlow. (2005) The Open Microscopy Environment (OME) Data Model and XML
file: open tools for informatics and quantitative analysis in biological
imaging. Genome Biology, v6, n5, pR47. |
| Provenance Ontology for Biological Images |
very new - used within their Provenance Management System for Biological Images (PROMISE) |
02 June 2005 |
|
Sudha Ram and Jun Liu (Department of Management Information Systems, University of Arizona, USA) - Nirav Merchant, Terrill Yuhas, and Patty Jansma (Arizona Research Laboratories, University of Arizona, USA) |
| Biological Imaging Methods‡ |
used in Drosophila Fly Base. |
02 June 2005 |
|
? |
| OBO Relations Ontology‡ |
provides a formally sound, foundational ontology for relations between types in all bio-medical ontologies submitted to OBO. These foundational relation types also can be used to formally specify relationships between ontology types and 'real-world' instances, in the creation of knowledge maps such as 'GO Association' files. |
14 November 2005 |
|
Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector and Cornelius Rosse (2005) Relations in Biomedical Ontologies. Genome Biology, v6, n5, pR46. |
†Included in the National Library of Medicine (NLM) Unified Medical Language System ( UMLS)
‡Included in list of Open Biological Ontologies site's list of "well-structured controlled vocabularies for shared use across different biological and medical domains".
¶Each semantic resource is classified according to four types of graph structure - flat list(FL), strict hierarchy (H), directed, acyclic graph (DAG) and complex ontology (CO).
aWe are quite distant at this point in time from supporting reasoning systems with rich knowledge maps built from highly granular, complex ontologies and accurate annotation/knowledge map construction algorithms. Given that fact, it's important to recognize our near-term use of onto-centric, knowledge maps will primarily be to support data integration & systems interoperability. One must recognize in that context even if the new ontological resource appears to cover knowledge domains in a much "superior" manner than existing resources covering the same domains (e.g., finer conceptual granularity, richer interconnectedness across domain branches, rules for driving automatic creation and analysis of knowledge maps, etc.), it will usually not be practical yet to use this improved semantic framework within the context of the Mouse BIRN Project. The reason is, where data integration & interoperability are concerned, ubiquity of use, rather than quality of ontological framework, is by far the higher priority. If it's possible to use the new ontology for building association/knowledge maps without incurring a large additional cost, and the maps made using the new ontology can be algorithmically mapped to the older, more common ontologies for that same knowledge domain, then it may be practical to move to using the new, "superior" semantic network. Otherwise, it is better to delay switching to this new ontology until it has garnered a significant amount of use throughout the fields generating the data sets we seek to integrate within the context of the Mouse BIRN project.
|
