VoCamp1 - Revision history

Hilmar: /* Overview */

2011-04-27T15:34:27Z

Overview

New page

<div style="font-weight: bold; font-size: large; margin-bottom: 20px; text-align: center">VoCamp Home</div>

This is the home page for the "Phyloinformatics VoCamp" workshop event scheduled to take place in coordination with the Biodiversity Information Standards (TDWG) meeting in Montpellier, France, in November, 2009.

== Overview ==

Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the [http://nescent.org National Evolutionary Synthesis Center] (NESCent) is sponsoring a "Phyloinformatics VoCamp".

The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It was be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

== Subgroups and Outcomes ==

The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):
# The [[Integrating Ontologies]] focused on specific data integration problems using CDAO, TDWG and other ontologies (John, Julie, Brandon, Rosemary, Peter, Stan, Rutger)
# [[Taxonomic Reasoning]] project took a more conceptual top-down approach to identifying needs in data integration (Dave T, Ann, David K, Raven, Dan, Mark S, Farshid)
# The [[Phyloreferencing_subgroup | Phyloreferencing]] group developed a rough draft of a spec for a PhyloWS language for querying trees (Hilmar, Josh, Nico, Sheldon, Karen, Bill, Arlin, Cate)
# The [[Publishing Taxonomies]] group aims to develop guidelines for publishing and consuming taxonomies (Roger, Jonathan, Greg)
# The [[TripleStore]] project focused on an AllegroGraph installation (Joel, Chris)
# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

On the afternoon of the 4th day we compiled [[VoCamp1/WrapUp| feedback and plans for follow-up]]. The event and its outcomes were also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.

== Resources and Links ==

VoCamp resources:
* [[VoCamp1/Participants| Participants]], with links to some of their projects
* [[VoCamp1/Schedule| Schedule]] of the event
* [[VoCamp1/Resources| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp
* [[VoCamp1/Background| Background & bootcamps]]
* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span>

Links and historical information
* pre-meeting [[VoCamp1/Pitches| list of possible pitches]]
* pre-meeting [[VoCamp1/Meeting Notes|teleconference notes]]
* [[VoCamp1/Proposal| Original VoCamp proposal]]
* [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetics Standards]

== Acknowledgements ==

The VoCamp event is an official activity of the [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetic Standards] and takes place through the generous support of [http://nescent.org NESCent], which funded a [[VoCamp1/Proposal| VoCamp proposal]] written by the organizers:
* Nico Cellinese
* Karen Cranston
* Hilmar Lapp
* Sheldon MacKay
* Enrico Pontelli
* Arlin Stoltzfus

The VoCamp proposal, in turn, builds on previous support from NESCent, which sponsored the [http://evoinfo.nescent.org Evolutionary Informatics Working Group]. The EvoInfo working group, which was active from 2006 to 2009, spawned the NeXML, CDAO and PhyloWS projects, and helped to organize 2 hackathons.

The organizers also thank [http://tdwg.org TDWG] and [http://www.lirmm.fr LIRMM] for their generous support. We are particularly grateful to Elizabeth Arnaud ([http://www.cgiar.org CGIAR]), Max Ruas ([http://www.cgiar.org CGIAR]), Brigitte Cabantous ([http://www.agropolis.fr Agropolis]), and Therese Libourel ([http://www.lirmm.fr LIRMM]) for their invaluable assistance throughout the organization of the VoCamp.

[[Category:Vocamp]]
[[Category:CDAO]]
[[Category:Metadata]]
[[Category:Standards]]
[[Category:NeXML]]
[[Category:Ontology]]

Hilmar: /* Subgroups and Outcomes */

2009-11-13T11:49:30Z

Subgroups and Outcomes

← Older revision		Revision as of 11:49, 13 November 2009
Line 19:		Line 19:
	# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data		# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

	The event and its outcomes were also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip\| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf\| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.		On the afternoon of the 4th day we compiled [[VoCamp1/WrapUp\| feedback and plans for follow-up]]. The event and its outcomes were also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip\| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf\| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.

	== Resources and Links ==		== Resources and Links ==

Hilmar: /* Subgroups and Outcomes */

2009-11-13T11:46:29Z

Subgroups and Outcomes

← Older revision		Revision as of 11:46, 13 November 2009
Line 19:		Line 19:
	# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data		# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

	The event and its outcomes ~~was~~ also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip\| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf\| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.		The event and its outcomes were also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip\| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf\| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.

	== Resources and Links ==		== Resources and Links ==

Hilmar: /* Acknowledgements */

2009-11-13T11:45:55Z

Acknowledgements

← Older revision		Revision as of 11:45, 13 November 2009
Line 38:		Line 38:
	== Acknowledgements ==		== Acknowledgements ==

	The VoCamp event is an official activity of the [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetic Standards] and takes place through the generous support of [http://nescent.org NESCent], which funded a [~~http:~~/~~/evoinfo.nescent.org/VoCamp1_Proposal~~ VoCamp proposal] written by the organizers:		The VoCamp event is an official activity of the [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetic Standards] and takes place through the generous support of [http://nescent.org NESCent], which funded a [[VoCamp1/Proposal\| VoCamp proposal]] written by the organizers:
	* Nico Cellinese		* Nico Cellinese
	* Karen Cranston		* Karen Cranston

Hilmar: /* Subgroups */

2009-11-13T11:43:43Z

Subgroups

← Older revision		Revision as of 11:43, 13 November 2009
Line 9:		Line 9:
	The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.		The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

	== Subgroups ==		== Subgroups and Outcomes ==

	The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):		The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):
Line 18:		Line 18:
	# The [[TripleStore]] project focused on an AllegroGraph installation (Joel, Chris)		# The [[TripleStore]] project focused on an AllegroGraph installation (Joel, Chris)
	# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data		# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

			The event and its outcomes was also presented (see [[Media:Phylo VoCamp report to TDWG.key.zip\| zip'ed Keynote]] and [[Media:Phylo VoCamp report to TDWG.pdf\| PDF versions]]) to the TDWG conference audience on Friday, Nov 13, two days after the end of the VoCamp.

	== Resources and Links ==		== Resources and Links ==

Hilmar at 11:08, 13 November 2009

2009-11-13T11:08:46Z

← Older revision		Revision as of 11:08, 13 November 2009
Line 3:		Line 3:
	This is the home page for the "Phyloinformatics VoCamp" workshop event scheduled to take place in coordination with the Biodiversity Information Standards (TDWG) meeting in Montpellier, France, in November, 2009.		This is the home page for the "Phyloinformatics VoCamp" workshop event scheduled to take place in coordination with the Biodiversity Information Standards (TDWG) meeting in Montpellier, France, in November, 2009.

	== ~~Quick links~~ ==		== Overview ==

			Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the [http://nescent.org National Evolutionary Synthesis Center] (NESCent) is sponsoring a "Phyloinformatics VoCamp".

			The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

			== Subgroups ==

	The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):		The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):
Line 13:		Line 19:
	# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data		# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

	~~Some other quick links~~:		== Resources and Links ==
	* [[~~VoCamp~~/Participants\| Participants]], with links to some of their projects
	* [[~~VoCamp~~/Resources\| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp		VoCamp resources:
	* [[~~VoCamp~~/Background\| Background & bootcamps]]		* [[VoCamp1/Participants\| Participants]], with links to some of their projects
			* [[VoCamp1/Schedule\| Schedule]] of the event
			* [[VoCamp1/Resources\| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp
			* [[VoCamp1/Background\| Background & bootcamps]]
	* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span>		* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span>

			Links and historical information
			* pre-meeting [[VoCamp1/Pitches\| list of possible pitches]]
			* pre-meeting [[VoCamp1/Meeting Notes\|teleconference notes]]
			* [[VoCamp1/Proposal\| Original VoCamp proposal]]
	* [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetics Standards]		* [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetics Standards]

	~~Historical interest~~
	* pre-meeting [[VoCamp/Pitches\| list of possible pitches]]
	* [http://evoinfo.nescent.org/VoCamp1_Proposal Original VoCamp proposal]
	* pre-meeting [[VoCamp/Meeting Notes\|teleconference notes]]

	~~== Overview ==~~

	Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the [http://nescent.org National Evolutionary Synthesis Center] (NESCent) is sponsoring a "Phyloinformatics VoCamp".

	The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

	== Acknowledgements ==		== Acknowledgements ==

Hilmar: /* Desired outcomes */

2009-11-13T10:50:29Z

Desired outcomes

← Older revision		Revision as of 10:50, 13 November 2009
Line 30:		Line 30:

	The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.		The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

	~~== Desired outcomes ==~~

	~~Desired outcomes for the period prior to the VoCamp~~
	* participants are aware of shared information resources, and know how to use them
	* participants (including organizers) know each other by name
	* participants know what is expected of them
	* participants identify and respond to information and training needs
	* participants discuss shared objectives and consider possible "pitches"

	~~Desired outcomes during Day 1 of the VoCamp~~
	* participants collectively formulate, present, review and revise "pitches"
	* participants self-organize into groups that will turn "pitches" into projects
	* participants choose a pitch that represents the best use of their time
	* groups assign roles and set goals

	~~Desired outcomes during Days 2, 3 and 4 of the VoCamp~~
	* groups work to advance group goals
	* groups report their progress during stand-ups and on the wiki
	* participants review other projects and offer constructive criticism

	== Acknowledgements ==		== Acknowledgements ==

Hilmar at 10:49, 13 November 2009

2009-11-13T10:49:32Z

New page

<div style="font-weight: bold; font-size: large; margin-bottom: 20px; text-align: center">VoCamp Home</div>

This is the home page for the "Phyloinformatics VoCamp" workshop event scheduled to take place in coordination with the Biodiversity Information Standards (TDWG) meeting in Montpellier, France, in November, 2009.

== Quick links ==

The VoCamp took place Nov 7 to 11 and resulted in 5 subgroup projects and 1 mini-project (links are in the sidebar):
# The [[Integrating Ontologies]] focused on specific data integration problems using CDAO, TDWG and other ontologies (John, Julie, Brandon, Rosemary, Peter, Stan)
# [[Taxonomic Reasoning]] project took a more conceptual top-down approach to identifying needs in data integration (Dave T, Ann, David K, Raven, Dan, Mark S, Farshid)
# The [[Phyloreferencing_subgroup | Phyloreferencing]] group developed a rough draft of a spec for a PhyloWS language for querying trees (Hilmar, Josh, Nico, Sheldon, Karen, Bill, Arlin, Cate)
# The [[Publishing Taxonomies]] group aims to develop guidelines for publishing and consuming taxonomies (Roger, Jonathan, Greg)
# The [[TripleStore]] project focused on an AllegroGraph installation (Joel, Chris)
# In a mini-project, Mark W extended the [[SADI]] system to integrate some biodiversity data

Some other quick links:
* [[VoCamp/Participants| Participants]], with links to some of their projects
* [[VoCamp/Resources| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp
* [[VoCamp/Background| Background & bootcamps]]
* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span>
* [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetics Standards]

Historical interest
* pre-meeting [[VoCamp/Pitches| list of possible pitches]]
* [http://evoinfo.nescent.org/VoCamp1_Proposal Original VoCamp proposal]
* pre-meeting [[VoCamp/Meeting Notes|teleconference notes]]

== Overview ==

Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the [http://nescent.org National Evolutionary Synthesis Center] (NESCent) is sponsoring a "Phyloinformatics VoCamp".

The Phyloinformatics VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of integration and semantic cross-linking of evolutionary data with its many related fields. It will be held on November 7-11, 2009 in Montpellier, France, co-localized with the annual meeting of the <span class="plainlinks">[http://www.tdwg.org/ International Biodiversity Information Standards Organization (TDWG)]</span>.

== Desired outcomes ==

Desired outcomes for the period prior to the VoCamp
* participants are aware of shared information resources, and know how to use them
* participants (including organizers) know each other by name
* participants know what is expected of them
* participants identify and respond to information and training needs
* participants discuss shared objectives and consider possible "pitches"

Desired outcomes during Day 1 of the VoCamp
* participants collectively formulate, present, review and revise "pitches"
* participants self-organize into groups that will turn "pitches" into projects
* participants choose a pitch that represents the best use of their time
* groups assign roles and set goals

Desired outcomes during Days 2, 3 and 4 of the VoCamp
* groups work to advance group goals
* groups report their progress during stand-ups and on the wiki
* participants review other projects and offer constructive criticism

== Acknowledgements ==

The VoCamp event is an official activity of the [http://www.tdwg.org/activities/phylogenetics/ TDWG Interest Group on Phylogenetic Standards] and takes place through the generous support of [http://nescent.org NESCent], which funded a [http://evoinfo.nescent.org/VoCamp1_Proposal VoCamp proposal] written by the organizers:
* Nico Cellinese
* Karen Cranston
* Hilmar Lapp
* Sheldon MacKay
* Enrico Pontelli
* Arlin Stoltzfus

The VoCamp proposal, in turn, builds on previous support from NESCent, which sponsored the [http://evoinfo.nescent.org Evolutionary Informatics Working Group]. The EvoInfo working group, which was active from 2006 to 2009, spawned the NeXML, CDAO and PhyloWS projects, and helped to organize 2 hackathons.

The organizers also thank [http://tdwg.org TDWG] and [http://www.lirmm.fr LIRMM] for their generous support. We are particularly grateful to Elizabeth Arnaud ([http://www.cgiar.org CGIAR]), Max Ruas ([http://www.cgiar.org CGIAR]), Brigitte Cabantous ([http://www.agropolis.fr Agropolis]), and Therese Libourel ([http://www.lirmm.fr LIRMM]) for their invaluable assistance throughout the organization of the VoCamp.

[[Category:Vocamp]]
[[Category:CDAO]]
[[Category:Metadata]]
[[Category:Standards]]
[[Category:NeXML]]
[[Category:Ontology]]

Hilmar: /* Travel, maps and logistics */

2009-10-29T22:40:26Z

Travel, maps and logistics

← Older revision		Revision as of 22:40, 29 October 2009
Line 74:		Line 74:
	'''Weather:'''		'''Weather:'''
	* Recent weather in Montpellier has been cloudy with showers and a daily high in the upper 60s F.		* Recent weather in Montpellier has been cloudy with showers and a daily high in the upper 60s F.
	** Current [http://www.wunderground.com/global/stations/07643.html weather in Montpellier]		* Current [http://www.wunderground.com/global/stations/07643.html weather in Montpellier]
	** Past weather, in terms of average daily highs and lows, has been:		* Past weather, in terms of average daily highs and lows, has been:
	*** October: daily high of 67 F (19 C), low of 53 F (12 C)		** October: daily high of 67 F (19 C), low of 53 F (12 C)
	*** November: daily high of 57 F (14 C), low of 42 F (6 C)		** November: daily high of 57 F (14 C), low of 42 F (6 C)

	== Acknowledgements ==		== Acknowledgements ==

Hilmar at 22:39, 29 October 2009

2009-10-29T22:39:46Z

← Older revision		Revision as of 22:39, 29 October 2009
Line 7:		Line 7:
	* [[VoCamp/Participants\| Participants]], with links to some of their projects		* [[VoCamp/Participants\| Participants]], with links to some of their projects
	* [[VoCamp/Pitches\| List of candidate projects]], contribute your idea		* [[VoCamp/Pitches\| List of candidate projects]], contribute your idea
	* [[VoCamp Resources\| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp		* [[VoCamp/Resources\| Resources related to the VoCamp]] such as ontologies and other artefacts to be used during the VoCamp
	* [[VoCamp/Background\| Background & bootcamps]]		* [[VoCamp/Background\| Background & bootcamps]]
	* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span> or our [[VoCamp/Meeting Notes\|meeting notes]]		* <span class="plainlinks">[https://lists.nescent.org/mailman/private/phylo-vocamp1 Mailing list archive]</span> or our [[VoCamp/Meeting Notes\|meeting notes]]