I am most familiar with using and working on the system in use with NLM NIH ontologies. A project or system that is meant to essentially jive with computer languages...
"Concepts expressed in the different parts of a Scientific article are to be linked to public Web ontologies, thus enabling the establishment of a formal relationship between the Scientific article specific knowledge base to ontologies like the UMLS – the Unified Medical Language System (http://www.nlm.nih.gov/pubs/factsheet/umls.html). The citations of an article are also be linked to the cited Web published scientific articles as qualified citations, in which the reasons to cite and the relationship between this specific scientific article and its citations are made explicit. The proposed model can enhances the scientific communication process, permitting semantic retrieval, critical inquiring, semantic citation, comparison, coherence verification and validating of a scientific article against public Web ontologies, which express the assented knowledge of a scientific area. The model was also conceived as the base for developing enhanced authoring and retrieval tools."
excerpt from Carlos Marcondes year 2005 title From Scientific Communication to Public Knowledge: the Scientific Article Web Published as a Knowledge Base source ELPUB2005. From Author to Reader: Challenges for the Digital Content Chain: Proceedings of the 9th ICCC International Conference on ElectronicPublishing held at Katholieke Universiteit Leuven in Leuven-Heverlee(Belgium), 8-10 June 2005 / Edited by: Milena Dobreva & Jan Engelen, ed. byPeeters Publishing Leuven, ISBN 90-429-1645-1, 2005 http://elpub.scix.net/cgi-bin/works/Show?_id=158elpub2005&sort=DEFAULT&search=year%3A2005&hits=69
however this Nature article concentrates on the onotolgies, rather than the ontologies hand in hand with the computer sciences, and it ultimately advocates
"Provide compliance with a standard upper ontology (SUO) developed by IEEE P1600.1. The ontology society has no accepted standard yet, SUMO, OpenCyc or a lattice of multiple upper ontologies, but any of them might be a reasonable guideline for construction of bio-ontologies."
A background paragraph from the Nature article on such...
The intersection between the ontologies listed at http://suo.ieee.org/SUO/Ontology-refs.html and those in the open biological ontologies repository (http://obo.sourceforge.net/cgi-bin/table.cgi) is the empty set.
A historical paragraph from the Nature article on MGED...
"The MGED Ontology was developed by MGED to provide descriptors required for MAGE v.1 (MicroArray and Gene Expression) documents. It is aimed to be the basis of the MIAME (Minimum Information About a Microarray Experiment) standard for capturing core information about microarray experiments and provides a conceptual structure for microarray experiment descriptions and annotation (Fig. 1). The MGED Ontology is one of the first attempts to formalize the description of experiments in biology"
I agree with the Nature article, that there must be an across the board system of standards and protocols, or there will be mayhem or confusion.
But competition seems to be keen, rightly so in a free market, to a certain extent, when there are the open source venues vying against non open source ontologies. Open source, such as the OBO (Open Biomedical Ontologies) Main (info) http://obo.sourceforge.net/
More info on NLM's UMLS
"NLM's Unified Medical Language System (UMLS) project develops and distributes multi-purpose, electronic "Knowledge Sources" and associated lexical programs for system developers. Researchers will find the UMLS products useful in investigating knowledge representation and retrieval questions." http://www.nlm.nih.gov/research/umls/
"Concepts expressed in the different parts of a Scientific article are to be linked to public Web ontologies, thus enabling the establishment of a formal relationship between the Scientific article specific knowledge base to ontologies like the UMLS – the Unified Medical Language System (http://www.nlm.nih.gov/pubs/factsheet/umls.html). The citations of an article are also be linked to the cited Web published scientific articles as qualified citations, in which the reasons to cite and the relationship between this specific scientific article and its citations are made explicit. The proposed model can enhances the scientific communication process, permitting semantic retrieval, critical inquiring, semantic citation, comparison, coherence verification and validating of a scientific article against public Web ontologies, which express the assented knowledge of a scientific area. The model was also conceived as the base for developing enhanced authoring and retrieval tools."
excerpt from
Carlos Marcondes
year 2005
title From Scientific Communication to Public Knowledge: the Scientific Article Web Published as a Knowledge Base
source ELPUB2005. From Author to Reader: Challenges for the Digital Content Chain: Proceedings of the 9th ICCC International Conference on ElectronicPublishing held at Katholieke Universiteit Leuven in Leuven-Heverlee(Belgium), 8-10 June 2005 / Edited by: Milena Dobreva & Jan Engelen, ed. byPeeters Publishing Leuven, ISBN 90-429-1645-1, 2005
http://elpub.scix.net/cgi-bin/works/Show?_id=158elpub2005&sort=DEFAULT&search=year%3A2005&hits=69
however this Nature article concentrates on the onotolgies, rather than the ontologies hand in hand with the computer sciences, and it ultimately advocates
"Provide compliance with a standard upper ontology (SUO) developed by IEEE P1600.1. The ontology society has no accepted standard yet, SUMO, OpenCyc or a lattice of multiple upper ontologies, but any of them might be a reasonable guideline for construction of bio-ontologies."
A background paragraph from the Nature article on such...
The intersection between the ontologies listed at http://suo.ieee.org/SUO/Ontology-refs.html and those in the open biological ontologies repository (http://obo.sourceforge.net/cgi-bin/table.cgi) is the empty set.
A historical paragraph from the Nature article on MGED...
"The MGED Ontology was developed by MGED to provide descriptors required for MAGE v.1 (MicroArray and Gene Expression) documents. It is aimed to be the basis of the MIAME (Minimum Information About a Microarray Experiment) standard for capturing core information about microarray experiments and provides a conceptual structure for microarray experiment descriptions and annotation (Fig. 1). The MGED Ontology is one of the first attempts to formalize the description of experiments in biology"
I agree with the Nature article, that there must be an across the board system of standards and protocols, or there will be mayhem or confusion.
But competition seems to be keen, rightly so in a free market, to a certain extent, when there are the open source venues vying against non open source ontologies. Open source, such as the OBO (Open Biomedical Ontologies) Main (info)
http://obo.sourceforge.net/
More info on NLM's UMLS
"NLM's Unified Medical Language System (UMLS) project develops and distributes multi-purpose, electronic "Knowledge Sources" and associated lexical programs for system developers. Researchers will find the UMLS products useful in investigating knowledge representation and retrieval questions."
http://www.nlm.nih.gov/research/umls/