publishing trees in CDAO as linked open data?
Dear all--
At the Biodiversity Information Standards (TDWG) meeting last month, a sub-group of the phylogenetic standards working group started a project to assess "current best practices for publishing trees electronically". At present, probably the best way to publish a tree is to use the TreeBASE submission process, which makes it possible to upload a NEXUS file and create associations of OTUs with taxon IDs, and of data rows with accessions, and so on. But there are also some other possibilities. The preliminary report is being assembled here:
http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010
Our plan is (over the next 6 weeks) to get feedback on this preliminary report, then analyze the results and prepare a more extensive report for publication.
One possibility that we haven't examined yet is to publish a tree electronically by rendering it in RDF in the language of CDAO (Comparative Data Analysis Ontology) and then contributing it to the Linked-Open-Data cloud in some way.
Does anyone out there want to explore this idea and contribute the results to the TDWG project? If so, please let me know.
Arlin ------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
I am interested in the sense that I think that TreeBASE should publish RDF renditions of its data in a LOD way.
On Mon, Oct 18, 2010 at 5:32 PM, Arlin Stoltzfus arlin@umd.edu wrote:
Dear all--
At the Biodiversity Information Standards (TDWG) meeting last month, a sub-group of the phylogenetic standards working group started a project to assess "current best practices for publishing trees electronically". At present, probably the best way to publish a tree is to use the TreeBASE submission process, which makes it possible to upload a NEXUS file and create associations of OTUs with taxon IDs, and of data rows with accessions, and so on. But there are also some other possibilities. The preliminary report is being assembled here:
http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010
Our plan is (over the next 6 weeks) to get feedback on this preliminary report, then analyze the results and prepare a more extensive report for publication.
One possibility that we haven't examined yet is to publish a tree electronically by rendering it in RDF in the language of CDAO (Comparative Data Analysis Ontology) and then contributing it to the Linked-Open-Data cloud in some way.
Does anyone out there want to explore this idea and contribute the results to the TDWG project? If so, please let me know.
Arlin
Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
tdwg-phylo mailing list tdwg-phylo@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
On Oct 18, 2010, at 12:32 PM, Arlin Stoltzfus wrote:
Does anyone out there want to explore this idea and contribute the results to the TDWG project? If so, please let me know.
Apropos of this, a fascinating reporting on the LOD cloud was just released, as described in the message below. Life science resources represent a sizable chunk of the cloud.
Arlin
---------- Forwarded message ---------- From: Anja Jentzsch anja@anjeve.de Date: Tue, Oct 19, 2010 at 10:33 AM Subject: ANN: LOD Cloud - Statistics and compliance with best practices To: "public-lod@w3.org" public-lod@w3.org
Hi all,
in the last weeks, we have analyzed which data sources in the new version of the LOD cloud comply to various best practices that are recommended by W3C or have emerged within the LOD community.
We have checked the implementation of the following nine best practices:
1. Provide dereferencable URIs 2. Set RDF links pointing at other data sources 3. Use terms from widely deployed vocabularies 4. Make proprietary vocabulary terms dereferencable 5. Map proprietary vocabulary terms to other vocabularies 6. Provide provenance metadata 7. Provide licensing metadata 8. Provide data-set-level metadata 9. Refer to additional access methods
The compliance with the best practices was either checked manually or by using scripts that downloaded and analyzed some data from the data sources. We have added the results of the evaluation in the form of tags to the LOD data set catalog on CKAN [1].
We are now happy to release the first statistics about the structure of the LOD could as well as the compliance of the datasets with the best practices. The statistics can be found here:
http://www4.wiwiss.fu-berlin.de/lodcloud/state/
The document contains an initial, preliminary release of the statistics. If you spot any errors in the data describing the LOD data sets on CKAN, it would be great if you would correct them directly on CKAN.
For information on how to describe datasets on CKAN please refer to the Guidelines for Collecting Metadata on Linked Datasets in CKAN [2].
After your feedback and corrections, we will then move the corrected version of the statistics to http://www.lod-cloud.net/ (around October 24th).
Have fun with the statistics and the encouraging as well as disappointing insights that they provide.
Cheers,
Chris Bizer, Anja Jentzsch and Richard Cyganiak
[1] http://www.ckan.net/group/lodcloud [2] http://esw.w3.org/TaskForces/CommunityProjects/LinkingOpenData/DataSets/CKAN...
------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
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