VoCamp1/Resources - Revision history

Hilmar at 11:10, 13 November 2009

2009-11-13T11:10:58Z

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	* [http://www.openspaceworld.org/ Open Space], Open Space Technology is a simple way to run productive meetings, for five to 2000+ people, and a powerful way to lead any kind of organization, in everyday practice and extraordinary change.		* [http://www.openspaceworld.org/ Open Space], Open Space Technology is a simple way to run productive meetings, for five to 2000+ people, and a powerful way to lead any kind of organization, in everyday practice and extraordinary change.
	* [http://www.shirky.com/writings/ontology_overrated.html Ontology is overrated] Clay Shirky article that Mark W. encourages us to read again and again		* [http://www.shirky.com/writings/ontology_overrated.html Ontology is overrated] Clay Shirky article that Mark W. encourages us to read again and again

			[[Category:Vocamp]]

Hilmar: moved VoCamp/Resources to VoCamp1/Resources

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moved VoCamp/Resources to VoCamp1/Resources

New page

[[VoCamp1|VoCamp Home...]]

==General Biological Ontologies==
* [http://mibbi.sourceforge.net/projects/MIAPA/ MIAPA] Minimal Information for Biological and Biomedical Investigations.

== Taxonomic Ontologies ==
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI Taxonomy]
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy Teleost Taxonomy Ontology]
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]
* [http://phenoscape.org/wiki/Taxonomic_Rank_Ontology Taxonomic Rank Ontology]

=== Ontologies for taxonomic, specimen, and species data ===

* [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome The Darwin Core] (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.
* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.

== Ontologies for scientific observations and experiments ==
* Extensible Observation Ontology (OBOE) A formal and conceptual framework for describing the semantics of observational data sets. Madin J, Bowers S, Schildhauer M, Krivov S, Pennington D, Villa F. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2: 279-296.
* [http://www.opengeospatial.org/standards/om Open Geospatial Consortium Obervations and Measurements (O&M)] The OpenGIS® Observations and Measurements Encoding Standard (O&M) defines an abstract model and an [www.w3.org/XML/Schema XML schema] encoding for observations and it provides support for common sampling strategies. O&M also provides a general framework for systems that deal in technical measurements in science and engineering.
* [https://sonet.ecoinformatics.org/ SONET] The Scientific Observations Network. NSF proposal to develop ontologies at the observation rather than dataset level.
* [http://obi-ontology.org/ Ontology for Biomedical Investigations], "an integrated ontology for the description of life-science and clinical investigations."

==Ecological/Enviromental Ontologies==
*[http://www5.umweltbundesamt.at/ALTERNet/index.php?title=Ont:ALTER-Net_Ontology|Socio-Ecological Research and Observation oNTology SERONTO]. This is the ontology being used by CEH and the ALTER to markup LTER data. [ftp://ftp.umweltbundesamt.at/LTER_Europe_Conference_Majorca08/Presentations/I3066v71_pres_magagna_ontology1.pdf Some slides on SERONTO]. [http://www.alter-net.info/SITE/UPLOAD/DOCUMENT/outputs/WPI6_2009_10_SERONTOCore.pdf Documentation].
*[http://www.aktors.org/technologies/f-life/ecolingua/ecolingua.html Ecolingua] With the intention of specifying an ontology for the description of ecological data, Brilhante and Robertson chose not to build the ontology from scratch, but to do it the `proper way', that is, by re-using publicly available ontologies of related fields and incorporating their specifications into Ecolingua. For this reason they turned to the library of sharable ontologies provided by the Ontolingua Server.
*[http://sweet.jpl.nasa.gov/index.html Earth sciences ontology] NASA Semantic Web for Earth and Environental Terminology (SWEET)
*[http://environmentontology.org/ The Environment Ontology (EnvO)] - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies

== Trait and Phenotype Ontologies ==
* [http://www.columbia.edu/cu/traitnet/index.html TraitNet] General ontology for traits.
* [http://www.amphibanat.org/ Amphibian Ontology]
* [http://www.animalgenome.org/bioinfo/projects/ATO/ Animal Trait Ontology project] - appears to only include ontology for pigs
* [http://www.informatics.jax.org/searches/MP_form.shtml Mammalian Phenotype] - based predominantly on mice and humans
* [http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality Phenotypic Qualities (PATO)]
* [http://zfin.org/zf_info/anatomy/dict/sum.html Zebrafish]
* [http://pantheon.generationcp.org/ontology/ GCP Crop Ontology (CO)] Controlled vocabularies for several crops, germplam and milti-crop passport data, molecular marker etc.

==Evolution Ontologies==
* [http://www.evolutionaryontology.org/ CDAO], "Comparative Data Analysis Ontology" and it is an initial tentative to formalize the most current used terms for evolutionary analysis in a single framework.

==Cellular Ontologies==

*Sequence Ontology (SO)
*Protein Ontology (PRO)
*Multiple Alignment Ontology (MAO)
*[http://genomebiology.com/2009/10/9/403 "quest for orthologs"]
*[http://bgee.unil.ch/download/homology_ontology.obo homology ontology]
*OBO relations ontology
*Ontology for Biomedical Investigations (OBI)
and many others.

==Geological Ontologies==
* [http://www.geongrid.org/index.php/geology/paleodata Palaeointegration project] provides extensive fossil and sedimentary rock databases that are searchable seamlessly from the GEON portal.

== Community resources ==

* [http://www.obofoundry.org/ Open Biomedical Ontologies] The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.
* [http://bioportal.bioontology.org/ NCBO BioPortal], indexes currently 170 ontologies with more than 720,000 concepts. There is also an [http://bioportal.bioontology.org/ontologies ontology browser] that, among other things, allows identifying ontologies by category.
* [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service], hosted at the EBI. Fast search and lookup of more or less all BioPortal ontologies.
* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.
* [http://vocabularies.gbif.org/ GBIF Vocabulary Server]
* [http://www.nescent.org/sites/hive/Main_Page HIVE (Helping Interdisciplinary Vocabulary Engineering)] - this is currently in development
* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.

== Links & Related resources ==

* [http://www.ohio.edu/phylocode/ PhyloCode], formal set of rules governing phylogenetic nomenclature.
* [http://www.nexml.org/ NeXML], an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process, and with a standards-compliant way to embed semantically rich metadata
* [http://evoinfo.nescent.org/PhyloWS PhyloWS], a standardized web-service API to allow integration of phylogenetic data and service providers into the programmable web.

'''Links'''
* [http://www.openspaceworld.org/ Open Space], Open Space Technology is a simple way to run productive meetings, for five to 2000+ people, and a powerful way to lead any kind of organization, in everyday practice and extraordinary change.
* [http://www.shirky.com/writings/ontology_overrated.html Ontology is overrated] Clay Shirky article that Mark W. encourages us to read again and again

Hilmar: /* Community resources */

2009-10-31T20:29:27Z

Community resources

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	* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.		* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.
	* [http://vocabularies.gbif.org/ GBIF Vocabulary Server]		* [http://vocabularies.gbif.org/ GBIF Vocabulary Server]
	* ~~{https~~://www.nescent.org/sites/hive/Main_Page HIVE (Helping Interdisciplinary Vocabulary Engineering)] - this is currently in development		* [http://www.nescent.org/sites/hive/Main_Page HIVE (Helping Interdisciplinary Vocabulary Engineering)] - this is currently in development
	* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.		* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.

Hilmar: /* Community resources */

2009-10-31T20:28:17Z

Community resources

← Older revision		Revision as of 20:28, 31 October 2009
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	* [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service], hosted at the EBI. Fast search and lookup of more or less all BioPortal ontologies.		* [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service], hosted at the EBI. Fast search and lookup of more or less all BioPortal ontologies.
	* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.		* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.
			* [http://vocabularies.gbif.org/ GBIF Vocabulary Server]
			* {https://www.nescent.org/sites/hive/Main_Page HIVE (Helping Interdisciplinary Vocabulary Engineering)] - this is currently in development
	* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.		* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.

Hilmar: /* Taxonomic Ontologies */

2009-10-31T20:12:41Z

Taxonomic Ontologies

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	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]
			* [http://phenoscape.org/wiki/Taxonomic_Rank_Ontology Taxonomic Rank Ontology]

	=== Ontologies for taxonomic, specimen, and species data ===		=== Ontologies for taxonomic, specimen, and species data ===

	* [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome The Darwin Core] (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.		* [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome The Darwin Core] (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.
	* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.		* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.

	== Ontologies for scientific observations and experiments ==		== Ontologies for scientific observations and experiments ==

Hilmar: /* Trait Ontologies */

2009-10-31T20:11:03Z

Trait Ontologies

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	*[http://environmentontology.org/ The Environment Ontology (EnvO)] - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies		*[http://environmentontology.org/ The Environment Ontology (EnvO)] - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies

	==Trait Ontologies==		== Trait and Phenotype Ontologies ==
	*[http://www.columbia.edu/cu/traitnet/index.html TraitNet] General ontology for traits.		* [http://www.columbia.edu/cu/traitnet/index.html TraitNet] General ontology for traits.
	*[http://www.amphibanat.org/ Amphibian Ontology]		* [http://www.amphibanat.org/ Amphibian Ontology]
	*[http://www.animalgenome.org/bioinfo/projects/ATO/ Animal Trait Ontology project] - appears to only include ontology for pigs		* [http://www.animalgenome.org/bioinfo/projects/ATO/ Animal Trait Ontology project] - appears to only include ontology for pigs
	*[http://www.informatics.jax.org/searches/MP_form.shtml Mammalian Phenotype] - based predominantly on mice and humans		* [http://www.informatics.jax.org/searches/MP_form.shtml Mammalian Phenotype] - based predominantly on mice and humans
	*[http://zfin.org/zf_info/anatomy/dict/sum.html Zebrafish]		* [http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
			* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality Phenotypic Qualities (PATO)]
			* [http://zfin.org/zf_info/anatomy/dict/sum.html Zebrafish]

	==Evolution Ontologies==		==Evolution Ontologies==

Hilmar: /* Observation Ontologies */

2009-10-31T20:09:03Z

Observation Ontologies

← Older revision		Revision as of 20:09, 31 October 2009
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	* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.		* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.

	==~~Observation~~ Ontologies==		== Ontologies for scientific observations and experiments ==
	*Extensible Observation Ontology (OBOE) A formal and conceptual framework for describing the semantics of observational data sets. Madin J, Bowers S, Schildhauer M, Krivov S, Pennington D, Villa F. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2: 279-296.		* Extensible Observation Ontology (OBOE) A formal and conceptual framework for describing the semantics of observational data sets. Madin J, Bowers S, Schildhauer M, Krivov S, Pennington D, Villa F. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2: 279-296.
	*Open Geospatial Consortium Obervations and Measurements (O&M) The OpenGIS® Observations and Measurements Encoding Standard (O&M) defines an abstract model and an [www.w3.org/XML/Schema XML schema] encoding for observations and it provides support for common sampling strategies. O&M also provides a general framework for systems that deal in technical measurements in science and engineering. ~~http://www.opengeospatial.org/standards/om~~		* [http://www.opengeospatial.org/standards/om Open Geospatial Consortium Obervations and Measurements (O&M)] The OpenGIS® Observations and Measurements Encoding Standard (O&M) defines an abstract model and an [www.w3.org/XML/Schema XML schema] encoding for observations and it provides support for common sampling strategies. O&M also provides a general framework for systems that deal in technical measurements in science and engineering.
	*[https://sonet.ecoinformatics.org/ SONET] The Scientific Observations Network. NSF proposal to develop ontologies at the observation rather than dataset level.		* [https://sonet.ecoinformatics.org/ SONET] The Scientific Observations Network. NSF proposal to develop ontologies at the observation rather than dataset level.
			* [http://obi-ontology.org/ Ontology for Biomedical Investigations], "an integrated ontology for the description of life-science and clinical investigations."

	==Ecological/Enviromental Ontologies==		==Ecological/Enviromental Ontologies==

Hilmar at 20:06, 31 October 2009

2009-10-31T20:06:34Z

← Older revision		Revision as of 20:06, 31 October 2009
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	[[VoCamp1\|VoCamp Home...]]		[[VoCamp1\|VoCamp Home...]]

	~~==Services==~~
	* [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome The Darwin Core] (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.
	* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.
	*[http://www.ohio.edu/phylocode/ PhyloCode], formal set of rules governing phylogenetic nomenclature.
	* [http://www.nexml.org/ NeXML], an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.
	* [https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS PhyloWS], a standardized web-service API to allow integration of phylogenetic data and service providers into the programmable web.
	*[http://www.openspaceworld.org/ Open Space], Open Space Technology is a simple way to run productive meetings, for five to 2000+ people, and a powerful way to lead any kind of organization, in everyday practice and extraordinary change.
	*[http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.
	*[http://www.obofoundry.org/ Open Biomedical Ontologies] The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.
	*[http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.

	==General Biological Ontologies==		==General Biological Ontologies==
	*[http://mibbi.sourceforge.net/projects/MIAPA/ MIAPA] Minimal Information for Biological and Biomedical Investigations.		* [http://mibbi.sourceforge.net/projects/MIAPA/ MIAPA] Minimal Information for Biological and Biomedical Investigations.

	==Taxonomic Ontologies==		== Taxonomic Ontologies ==
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI Taxonomy]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI Taxonomy]
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy Teleost Taxonomy Ontology]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy Teleost Taxonomy Ontology]
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]

			=== Ontologies for taxonomic, specimen, and species data ===

			* [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome The Darwin Core] (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. Extensions to the Darwin Core provide a mechanism to share additional information, which may be discipline-specific, or beyond the commonly agreed upon scope of the Darwin Core itself.
			* The [http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology TDWG ontology] from Biodiversity Information Standards ([http://tdwg.org TDWG]), an international not-for-profit group that develops standards and protocols for sharing biodiversity data.

	==Observation Ontologies==		==Observation Ontologies==
Line 42:		Line 36:
	* [http://www.evolutionaryontology.org/ CDAO], "Comparative Data Analysis Ontology" and it is an initial tentative to formalize the most current used terms for evolutionary analysis in a single framework.		* [http://www.evolutionaryontology.org/ CDAO], "Comparative Data Analysis Ontology" and it is an initial tentative to formalize the most current used terms for evolutionary analysis in a single framework.

	==Cellular? Ontologies==		==Cellular Ontologies==

	*Sequence Ontology (SO)		*Sequence Ontology (SO)
	*Protein Ontology (PRO)		*Protein Ontology (PRO)
Line 49:		Line 44:
	*[http://bgee.unil.ch/download/homology_ontology.obo homology ontology]		*[http://bgee.unil.ch/download/homology_ontology.obo homology ontology]
	*OBO relations ontology		*OBO relations ontology
	*Ontology for Biomedical Investigations (OBI)and many others.		*Ontology for Biomedical Investigations (OBI)
			and many others.

	==Geological Ontologies==		==Geological Ontologies==
	* [http://www.geongrid.org/index.php/geology/paleodata Palaeointegration project] provides extensive fossil and sedimentary rock databases that are searchable seamlessly from the GEON portal.		* [http://www.geongrid.org/index.php/geology/paleodata Palaeointegration project] provides extensive fossil and sedimentary rock databases that are searchable seamlessly from the GEON portal.

			== Community resources ==

			* [http://www.obofoundry.org/ Open Biomedical Ontologies] The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.
			* [http://bioportal.bioontology.org/ NCBO BioPortal], indexes currently 170 ontologies with more than 720,000 concepts. There is also an [http://bioportal.bioontology.org/ontologies ontology browser] that, among other things, allows identifying ontologies by category.
			* [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service], hosted at the EBI. Fast search and lookup of more or less all BioPortal ontologies.
			* [http://www.bodc.ac.uk/products/web_services/vocab/ NERC DataGrid vocabulary server] The NDG vocabulary server provides access to lists of standardised terms that cover a broad spectrum of disciplines of relevance to the oceanographic and wider community.
			* [http://www.ksl.stanford.edu/software/ontolingua/ Ontolingua] - a distributed collaborative environment to browse, create, edit, modify, and use ontologies.

			== Links & Related resources ==

			* [http://www.ohio.edu/phylocode/ PhyloCode], formal set of rules governing phylogenetic nomenclature.
			* [http://www.nexml.org/ NeXML], an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process, and with a standards-compliant way to embed semantically rich metadata
			* [http://evoinfo.nescent.org/PhyloWS PhyloWS], a standardized web-service API to allow integration of phylogenetic data and service providers into the programmable web.

			'''Links'''
			* [http://www.openspaceworld.org/ Open Space], Open Space Technology is a simple way to run productive meetings, for five to 2000+ people, and a powerful way to lead any kind of organization, in everyday practice and extraordinary change.

Hilmar: /* Ecological/Enviromental Ontologies */

2009-10-31T19:45:04Z

Ecological/Enviromental Ontologies

← Older revision		Revision as of 19:45, 31 October 2009
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	*[http://www.aktors.org/technologies/f-life/ecolingua/ecolingua.html Ecolingua] With the intention of specifying an ontology for the description of ecological data, Brilhante and Robertson chose not to build the ontology from scratch, but to do it the `proper way', that is, by re-using publicly available ontologies of related fields and incorporating their specifications into Ecolingua. For this reason they turned to the library of sharable ontologies provided by the Ontolingua Server.		*[http://www.aktors.org/technologies/f-life/ecolingua/ecolingua.html Ecolingua] With the intention of specifying an ontology for the description of ecological data, Brilhante and Robertson chose not to build the ontology from scratch, but to do it the `proper way', that is, by re-using publicly available ontologies of related fields and incorporating their specifications into Ecolingua. For this reason they turned to the library of sharable ontologies provided by the Ontolingua Server.
	*[http://sweet.jpl.nasa.gov/index.html Earth sciences ontology] NASA Semantic Web for Earth and Environental Terminology (SWEET)		*[http://sweet.jpl.nasa.gov/index.html Earth sciences ontology] NASA Semantic Web for Earth and Environental Terminology (SWEET)
	*[http://environmentontology.org/ The Environment Ontology] - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies		*[http://environmentontology.org/ The Environment Ontology (EnvO)] - Describes classes such as 'coastal' and 'woodland' and how they relate between different ontologies

	==Trait Ontologies==		==Trait Ontologies==

Hilmar: /* Taxonomic Ontologies */

2009-10-31T19:44:04Z

Taxonomic Ontologies

← Older revision		Revision as of 19:44, 31 October 2009
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	==Taxonomic Ontologies==		==Taxonomic Ontologies==
	*NCBI~~'s taxids~~		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI Taxonomy]
	* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy Teleost Taxonomy Ontology]		* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy Teleost Taxonomy Ontology]
			* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_taxonomy Amphibian Taxonomy Ontology]
			* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy Fly Taxonomy]

	==Observation Ontologies==		==Observation Ontologies==