A Survey of Ontology Usage in Academic Sciences: Informal Ontologies

Please also see SurveyFormalOntologies.

Biology / Biomedicine

Phylogenies

“The genesis and evolution of the phylum, tribe, or species; ancestral or racial evolution of an animal or plant type, or of particular organs or other components of a plant or an animal.” - Oxford English Dictionary

Phylogeny Links:

• http://evolution.berkeley.edu/evosite/evo101/IIBPhylogenies.shtml - Evolution 101 - Understanding phylogenies

Phylogeny Papers:

• Tree of Life project - http://www.brightsurf.com/news/nov_02/EDU_news_111302_b.html
• Blanchette, M. and M. Tompa. 2003. FootPrinter : a program designed for phylogenetic footprinting. Nucleic Acids Research 31: 3840-3842., http://nar.oxfordjournals.org/cgi/reprint/31/13/3840.pdf
• Blanchette, M. and M. Tompa. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 12: 739-748., http://www.cs.washington.edu/homes/blanchem/mypapers/GR/gr.pdf
• Blanchette, M., B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology 9: 211-223., http://www.cs.washington.edu/homes/blanchem/mypapers/RECOMB01/recomb.pdf

Phylogeny Software:

• http://evolution.genetics.washington.edu/phylip/software.html - repository of links to hundreds of phylogeny programs. These algorithms infer evolutationary trees from various organism characteristics. Common methods include parsimony, R statistics, generalized least squares,

Library Systems

Dewey Decimal

Dewey Decimal Links:

• http://en.wikipedia.org/wiki/Dewey_Decimal_Classification - Wikipedia entry on Dewey Decimal cataloguing system
• http://www.oclc.org/dewey/ - OCLC's Dewey Decimal homepage

Dewey Decimal Papers:

• http://www.oclc.org/dewey/versions/ddc22print/ - Unabridged Dewey Decimal classification system
• http://64.233.167.104/search?q=cache:ZSExeVzJmHEJ:www.sabinet.co.za/cataloguing/cat_img/ddc_newsliasa.doc+%22dewey+decimal%22+software+cataloguing&hl=en - Dewey Decimal newsletter
• http://valinor.ca/lis601_marc.html - Anglo American Cataloguer's Rules
• http://www.ifla.org/IV/ifla64/083-126e.htm - Anglo American Cataloguer's Rules with relation to digital libraries and archives

Dewey Decimal Software:

• http://www.oclc.org/connexion/ - Connexion (commercial software)

Library of Congress

Library of Congress Links:

• http://en.wikipedia.org/wiki/Library_of_Congress_Classification - Wikipedia entry on Library of Congress cataloguing system
• http://www.loc.gov/catdir/cpso/lcco/lcco.html - List of major classification topics
• http://www.loc.gov/marc/ - MARC standards: machine-readable bibliographic / curation information used in the US and Canada, including the "MARC to Dublin Core Crosswalk": http://www.loc.gov/marc/marc2dc.html. Also includes links to UKMARC: http://www.bl.uk/services/bibliographic/marc/marcman.html, used in the UK.
• http://www.loc.gov/cds/downloads/FRBR.PDF - library pamphlet explain some useful acronyms

Library of Congress Papers:

• http://www.loc.gov/rr/print/tgm1/ - Thesaurus for Graphical Materials
• http://www.loc.gov/cds/classif.html - LoC classification schedules and manuals

Library of Congress Software:

• http://www.loc.gov/marc/marctools.html - MARC specialized tools
• http://marcpm.sourceforge.net/ - MARC/Perl, software for manipulation of bibliographic records from sourceforge
• http://www.loc.gov/standards/premis/ - PREMIS, Preservation Metadata. Links to schemas, data dictionary, implementation.
• http://www.loc.gov/standards/marcxml/ - MARCXML
• http://www.loc.gov/marc/marc-functional-analysis/tool.html - FRBR (Functional Requirements for Bibliographic Records) tool
• http://www.loc.gov/catdir/cpso/cpso.html#tools - LoC Cataloguing tools and documentation

Generic Ontology Links

• http://ontology.buffalo.edu/ - philosopy department, collectors of ontologies

Not an Ontology

• http://www.answers.com/topic/bohm-interpretation - the Bohm Ontology Interpretation of quantum mechanics (It's ontological, Jim, but not as we know it.)
• http://www.wired.com/news/technology/0,1282,55509,00.html - Library of Congress Taps the Grid
• http://www.loc.gov/catworkshop/ - Cataloguer's Learning Workshop, online clearinghouse for metadata learning

-- ElizabethAuden - 02 Aug 2005