A Survey of Ontology Usage in Academic Sciences: Formal Ontologies

Please also see SurveyInformalOntologies.

Biology / Biomedicine

GO, Gene Ontology

“The goal of the Gene Ontology project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes.” - GO homepage

The Gene Ontology provides a vocabulary of genetic annotation terms covering three areas:

• molecular function – acitivities that happen at the molecular level
• biological process - sequences of molecular functions that happen in a specific order in biological entities
• cellular component – pieces of a cell’s anatomy or gene groups

By organizing gene annotations into an ontology with tens of thousands of terms, the GO consortium hopes to speed up the time it takes to identify genetic products and their functions, accurately group genes and other cell components together based on function, and lower the number of false positives when classifying genetic products and functions.

Download GO ontology

• http://archive.godatabase.org/latest-termdb/go_daily-termdb.owl.gz

This link provides a gzipped OWL-formatted ontology of the GO terms and relationships. Updated daily.

GO Links

• http://www.geneontology.org/ - Gene Ontology Consortium page

GO Papers

1. Bluthgen, Nils et al. “Biological Profiling of Gene Groups Utilizing Gene Ontology – A Statistical Framework.” 9 May 2005. (web) http://arxiv.org/PS_cache/q-bio/pdf/0407/0407034.pdf
2. Bluthgen, Nils et al. “GOSSIP: Biological Profiling of Gene Groups Utilizing Gene Ontology .“ (poster) http://itb.biologie.hu-berlin.de/~nils/poster_bielefeld.pdf
3. Szymon M. Kielbasa, Nils Blüthgen, and Hanspeter Herzel: Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors In: R. Giegerich, J. Stoye (eds.): German Conference on Bioinformatics - Bonn 2004: Koellen Druck+Verlag, pages 105-113.
4. Nils Blüthgen, Szymon M. Kielbasa, and Hanspeter Herze: Inferring Combinatorial Regulation of Transcription in silico Nucleic Acids Research 33 (2005):272-279.

GO Software

• GOSSIP: http://gossip.gene-groups.net/
• Onto-Express: http://vortex.cs.wayne.edu/Onto-Tools%20User%20Manual/Onto-Express/Onto-Express.html
• EASE+David: http://apps1.niaid.nih.gov/david/
• GoSurfer : http://www.biostat.harvard.edu/complab/gosurfer/
• GoMiner : http://discover.nci.nih.gov/gominer/
• GeneMerge : http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge/GeneMerge.html
• GOAT - http://goat.man.ac.uk/ (Gene Ontology Anotation Tool)

OBO, Open Biomedical Ontologies

Download OBO ontologies

• http://obo.sourceforge.net/cgi-bin/table.cgi

This link provides a table of all biolomedical ontologies using the OBO format and uploaded to the OBO sourceforge repository. Topics include cells, proteins, botany, animal sciences, medicine, genes, and more. The Gene Ontology is a subset of the OBO ontologies.

OBO Links:

• http://obo.sourceforge.net/ - Open Biomedical Ontologies page

OBO Papers:

• "Linking the Gene Ontology to other biological ontologies", http://mor.nlm.nih.gov/pubs/pdf/2005-ismb_bioontologies-ob.pdf

OBO Software:

• http://www.godatabase.org/dev/java/dagedit/docs/ - DAG-Edit software

Oncology Ontology

Download Oncology ontology: N/A

Ontology Oncology Links: N/A

Oncology Ontology papers:

• "Oncology Ontology in the NCI Thesaurus", http://ontology.buffalo.edu/medo/NCITcolon.pdf

Oncology Ontology Software: N/A

Environmental and Space Sciences

VSTO - Virtual Solar Terrestrial Observatory

Download VSTO ontologies: N/A

• http://dataportal.ucar.edu/schemas/vsto_all.owl
• http://dataportal.ucar.edu/schemas/vsto.owl
• http://dataportal.ucar.edu/schemas/cedar.owl
• http://dataportal.ucar.edu/schemas/mlso.owl

VSTO Links: N/A

• http://vsto.hao.ucar.edu/use_cases.php
• http://vsto.hao.ucar.edu/index.php

VSTO papers:

• "Ontology-Enabled Virtual Observatories: Semantic Integration in Practice", http://vsto.hao.ucar.edu/presentations/ISWC2006_poster20061103.pdf
• "Semantically-Enabled Virtual Observatories", http://vsto.hao.ucar.edu/presentations/20061010OWLEdMcGuinnessSemanticallyEnabledVirtualObservatories.pdf
• "Semantically-Enabled Large-Scale Science Data Repositories", http://vsto.hao.ucar.edu/presentations/ISWC2006_SDI_Fox.pdf

VSTO Software: N/A

• VSTO data portal: http://www.vsto.org/home/home.htm

Geography, Geology and Hydrology Papers

• "Requirements for Geospatial Ontology Engineering", http://ifgi.uni-muenster.de/~klien/publications/KlienProbst05_RequirementsForGOE.pdf
• Geographical ontology proposal: http://www.geog.ucsb.edu/~good/275/v2kontology2.htm
• "From Geo to Eco Ontologies", http://www.spatial.maine.edu/~fred/Fonseca_Martin_Rodriguez.pdf
• "Architecture for Ontology-Based Discovery and Retrieval of Geographic Information", http://ifgi.uni-muenster.de/~lutzm/agile04_klien_et_al.pdf

Space Science Papers

• "An Ontology to Support Knowledge Enabled Services on Earth Observation", http://earth.esa.int/rtd/Events/ESA-EUSC_2004/Ar18_Pereira.pdf

Libraries and Curation

Dublin Core

Download Dublin Core ontology:

• http://www.cs.umd.edu/projects/plus/SHOE/onts/dublin.html (SHOE format)
• http://protege.cim3.net/file/pub/ontologies/dublin-core/hcm_dc_in_protege.zip (Protegé format)
• http://orlando.drc.com/SemanticWeb/owl/ontology/DC/dces-ont (RDF format - old)

Dublin Core Links:

• Using Dublin Core: http://dublincore.org/documents/usageguide/bibliography.shtml

Dublin Core recommendations:

• "Expressing Dublin Core metadata using the Resource Description Language", http://dublincore.org/documents/2007/06/04/dc-rdf/
• "Expressing Dublin Core metadata using HTML / XHTML meta and link elements", http://dublincore.org/documents/2007/11/05/dc-html/

Dublin Core ontology software:

• Dublin Core tools: http://dublincore.org/tools/

-- ElizabethAuden - 02 Aug 2005