MIAPA - Revision history

Hilmar at 22:14, 1 June 2018

2018-06-01T22:14:47Z

← Older revision		Revision as of 22:14, 1 June 2018
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	* [http://mibbi.sourceforge.net/projects/MIAPA.shtml MIAPA at MIBBI]		* [http://mibbi.sourceforge.net/projects/MIAPA.shtml MIAPA at MIBBI]
	* [[CommentsOnOpenAnnotationDataModel]]		* [[CommentsOnOpenAnnotationDataModel]]
	* [https://~~www~~.nescent.org~~/wg_evoinfo~~/MIAPA_WhitePaper MIAPA white paper] at NESCent		* [https://evoinfo.nescent.org/MIAPA_WhitePaper MIAPA white paper] at NESCent
	* Arlin's [https://~~www~~.nescent.org~~/wg_evoinfo~~/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]		* Arlin's [https://evoinfo.nescent.org/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
	* Leebens-Mack et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS: a Journal of Integrative Biology 10 (2): 231-7. [http://dx.doi.org/10.1089/omi.2006.10.231 doi:10.1089/omi.2006.10.231].		* Leebens-Mack et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS: a Journal of Integrative Biology 10 (2): 231-7. [http://dx.doi.org/10.1089/omi.2006.10.231 doi:10.1089/omi.2006.10.231].

	[[Category:MIAPA]]		[[Category:MIAPA]]

Hilmar: /* Current version of the MIAPA checklist */

2018-06-01T22:12:32Z

Current version of the MIAPA checklist

New page

This serves as a web home and central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

== Current versions ==

The most current versions of MIAPA artifacts such as checklist, ontologies, and tools are maintained on Github: https://github.com/evoinfo/miapa

* [https://github.com/evoinfo/miapa/blob/master/checklist/MIAPA-checklist.md MIAPA checklist]
* [https://github.com/evoinfo/miapa/blob/master/ontology/miapa.owl MIAPA ontology] ([https://raw.githubusercontent.com/evoinfo/miapa/master/ontology/miapa.owl OWL format])

== Links ==

'''Active projects'''
* Karen Cranston and Elliot Hauser surveyed the community about the the MIAPA checklist terms
** [https://duke.qualtrics.com/SE/?SID=SV_b2upIMII4fxJkAA link to survey]
** resulting manuscript is in preparation on [https://github.com/eah13/otol GitHub]
* Elliott Hauser's 2012 Google Summer of Code project "[http://informatics.nescent.org/wiki/PhyloSoC:_NeXML_to_MIAPA_mapping NeXML to MIAPA mapping]"
* Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
** This workshop produced a [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey checklist of metadata elements] for a proposed community survey.
* [[MIAPA Draft RFC]]
* Plan for a [[PhyloRelevantLiteratureSurvey]]
* [[Conference Plan 2011]]
* [[Tree Best Practices]], article in progress for BMC, based largely on TDWG report
* [[MIAPA Survey]] on barriers to re-use of phylogenies and associated data and metadata
** [[Reuse Cases]]
** [[Barriers to reuse]] -- from user stories collected by the survey team
** [[Reuse Barriers]] -- Hilmar's list regarding TreeBASE submissions
* [[MIAPA/Demonstration Project| MIAPA Demonstration Project]] in the Leebens-Mack lab, spring 2011
* The [[MIAPA/PhyloWays| PhyloWays]] list of reference workflow annotations (papers with extracted workflow information)

'''Resources'''
* There is an [http://groups.google.com/group/miapa-discuss email list] for discussion of MIAPA. Please consider joining if you would like to play an active role in developing and supporting a minimal-information checklist for phylogenetic studies.
* [http://mibbi.sourceforge.net/projects/MIAPA.shtml MIAPA at MIBBI]
* [[CommentsOnOpenAnnotationDataModel]]
* [https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper MIAPA white paper] at NESCent
* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
* Leebens-Mack et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS: a Journal of Integrative Biology 10 (2): 231-7. [http://dx.doi.org/10.1089/omi.2006.10.231 doi:10.1089/omi.2006.10.231].

[[Category:MIAPA]]

Hilmar: /* Links */

2013-01-28T23:26:57Z

Links

← Older revision		Revision as of 23:26, 28 January 2013
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	'''Active projects'''		'''Active projects'''
	* Elliott Hauser's 2012 Google Summer of Code project "[http://informatics.nescent.org/wiki/PhyloSoC:_NeXML_to_MIAPA_mapping NeXML to MIAPA mapping]"		* Elliott Hauser's 2012 Google Summer of Code project "[http://informatics.nescent.org/wiki/PhyloSoC:_NeXML_to_MIAPA_mapping NeXML to MIAPA mapping]"
			* Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
	* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011		* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
	** This workshop produced a [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey checklist of metadata elements] for a proposed community survey.		** This workshop produced a [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey checklist of metadata elements] for a proposed community survey.

Hilmar: /* Links */

2013-01-28T22:51:49Z

Links

New page

This serves as a web home and central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

== Links ==

'''Active projects'''
* Elliott Hauser's 2012 Google Summer of Code project "[http://informatics.nescent.org/wiki/PhyloSoC:_NeXML_to_MIAPA_mapping NeXML to MIAPA mapping]"
* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
** This workshop produced a [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey checklist of metadata elements] for a proposed community survey.
* [[MIAPA Draft RFC]]
* Plan for a [[PhyloRelevantLiteratureSurvey]]
* [[Conference Plan 2011]]
* [[Tree Best Practices]], article in progress for BMC, based largely on TDWG report
* [[MIAPA Survey]] on barriers to re-use of phylogenies and associated data and metadata
** [[Reuse Cases]]
** [[Barriers to reuse]] -- from user stories collected by the survey team
** [[Reuse Barriers]] -- Hilmar's list regarding TreeBASE submissions
* [[MIAPA/Demonstration Project| MIAPA Demonstration Project]] in the Leebens-Mack lab, spring 2011
* The [[MIAPA/PhyloWays| PhyloWays]] list of reference workflow annotations (papers with extracted workflow information)

'''Resources'''
* There is an [http://groups.google.com/group/miapa-discuss email list] for discussion of MIAPA. Please consider joining if you would like to play an active role in developing and supporting a minimal-information checklist for phylogenetic studies.
* [https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper MIAPA white paper] at NESCent
* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
* Leebens-Mack et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS: a Journal of Integrative Biology 10 (2): 231-7. [http://dx.doi.org/10.1089/omi.2006.10.231 doi:10.1089/omi.2006.10.231].

[[Category:MIAPA]]

Hilmar: /* Links */

2012-05-09T22:13:58Z

Links

← Older revision		Revision as of 22:13, 9 May 2012
Line 4:		Line 4:

	'''Active projects'''		'''Active projects'''
			* Elliott Hauser's 2012 Google Summer of Code project "[http://informatics.nescent.org/wiki/PhyloSoC:_NeXML_to_MIAPA_mapping NeXML to MIAPA mapping]"
	* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011		* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
	* [[MIAPA Draft RFC]]		* [[MIAPA Draft RFC]]

Hilmar: /* Links */

2012-02-10T06:47:59Z

Links

← Older revision		Revision as of 06:47, 10 February 2012
Line 20:		Line 20:
	* [https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper MIAPA white paper] at NESCent		* [https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper MIAPA white paper] at NESCent
	* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]		* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
	* [http://~~www~~.~~liebertonline~~.~~com~~/doi~~/abs/~~10.1089/omi.2006.10.231 ~~Leebens-Mack, et al, 2006~~]		* Leebens-Mack et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS: a Journal of Integrative Biology 10 (2): 231-7. [http://dx.doi.org/10.1089/omi.2006.10.231 doi:10.1089/omi.2006.10.231].

	[[Category:MIAPA]]		[[Category:MIAPA]]

Hilmar at 06:44, 10 February 2012

2012-02-10T06:44:37Z

← Older revision		Revision as of 06:44, 10 February 2012
Line 4:		Line 4:

	'''Active projects'''		'''Active projects'''
	* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/ Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011		* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPAWorkshop2011 Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
	* [[MIAPA Draft RFC]]		* [[MIAPA Draft RFC]]
	* plan for a [[PhyloRelevantLiteratureSurvey]]		* plan for a [[PhyloRelevantLiteratureSurvey]]

Hilmar at 06:44, 10 February 2012

2012-02-10T06:44:20Z

New page

This serves as a web home and central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

== Links ==

'''Active projects'''
* [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/ Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard] workshop at TDWG 2011
* [[MIAPA Draft RFC]]
* plan for a [[PhyloRelevantLiteratureSurvey]]
* [[Conference Plan 2011]]
* [[Tree Best Practices]], article in progress for BMC, based largely on TDWG report
* [[MIAPA Survey]] on barriers to re-use of phylogenies and associated data and metadata
** [[Reuse Cases]]
** [[Barriers to reuse]] -- from user stories collected by the survey team
** [[Reuse Barriers]] -- Hilmar's list regarding TreeBASE submissions
* [[MIAPA/Demonstration Project| MIAPA Demonstration Project]] in the Leebens-Mack lab, spring 2011
* The [[MIAPA/PhyloWays| PhyloWays]] list of reference workflow annotations (papers with extracted workflow information)

'''Resources'''
* There is an [http://groups.google.com/group/miapa-discuss email list] for discussion of MIAPA. Please consider joining if you would like to play an active role in developing and supporting a minimal-information checklist for phylogenetic studies.
* [https://www.nescent.org/wg_evoinfo/MIAPA_WhitePaper MIAPA white paper] at NESCent
* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
* [http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.231 Leebens-Mack, et al, 2006]

[[Category:MIAPA]]

Hilmar at 14:09, 1 August 2011

2011-08-01T14:09:08Z

← Older revision		Revision as of 14:09, 1 August 2011
Line 20:		Line 20:
	* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]		* Arlin's [https://www.nescent.org/wg_evoinfo/Supporting_MIAPA proof-of-concept and an idea for a knowledge-capture experiment]
	* [http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.231 Leebens-Mack, et al, 2006]		* [http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.231 Leebens-Mack, et al, 2006]

			[[Category:MIAPA]]

Hilmar: /* Links */

2011-08-01T13:59:24Z

Links

← Older revision		Revision as of 13:59, 1 August 2011
Line 10:		Line 10:
	* [[MIAPA Survey]] on barriers to re-use of phylogenies and associated data and metadata		* [[MIAPA Survey]] on barriers to re-use of phylogenies and associated data and metadata
	** [[Reuse Cases]]		** [[Reuse Cases]]
	** [[Barriers to ~~Reuse~~]] -- from user stories collected by the survey team		** [[Barriers to reuse]] -- from user stories collected by the survey team
	** [[Reuse Barriers]] -- Hilmar's list regarding TreeBASE submissions		** [[Reuse Barriers]] -- Hilmar's list regarding TreeBASE submissions
	* [[MIAPA/Demonstration Project\| MIAPA Demonstration Project]] in the Leebens-Mack lab, spring 2011		* [[MIAPA/Demonstration Project\| MIAPA Demonstration Project]] in the Leebens-Mack lab, spring 2011