Webinars "iDigBio and Using schema.org and microdata for data discovery" 2014-04-15 at 1600 EDT

The topics for the next C4P Webinar are iDigBio (Gil Nelson, Florida State University) and Using schema.org and microdata for data discovery (Douglas Fils, Ocean Leadership Consortium).

The link to the webinar is

WebEx link for April 15, 4-5p ET (the date stated at the link updates weekly)

If a password is required, enter the Meeting Password: 73131647

For plain text postings where the link did not show up: Any updated links or information as well as the updated webinar schedule and archived presentations will be posted at

http://workspace.earthcube.org/c4p/content/c4p-webinars

iDigBio (Gil Nelson, Florida State University)

http://www.idigbio.org

Integrated Digitized Biocollections (iDigBio) is NSF's national resource for facilitating and enabling the digitization of biological and paleobiological collection objects in non-federal, U.S. biodiversity collections. Through its portal it makes available data and images for millions of biological specimens in electronic format for the research community, government agencies, students, educators, and the general public.

Using schema.org and microdata for data discovery (Douglas Fils, Consortium for Ocean Leadership)

HTML5 developments in the area of microdata have provided methods for resource discovery based on structured data embedded into HTML pages.  Combined with the schema.org Dataset and other vocabularies this facilitates a means to bring structured data about scientific data resources to web pages.  This talk will demonstrate examples of these patterns applied to data.oceandrilling.org and other sites.  It will further provide live examples of these patterns and discuss methods that could be used to enhance domain specific data offerings.  

The format is 20 minutes per presenter, with two main parts: (a) a show-and-tell presentation of the science and the resource (b) discussion of the key informatics needs that the resource is facing. The intended audience for this webinar is professional paleogeoscientists and cyber/computer scientists.  All webinars will be recorded and publicly archived at http://workspace.earthcube.org/c4p/content/c4p-webinars.

More about C4P:

Website: http://workspace.earthcube.org/c4p

Technical information for webinars: cyber4paleo@gmail.com

TaxonConcept's Taxon Concepts II

Well, it is done ;) Here is an example which shows how our TCS XML looks like:
http://taxonconcept.stratigraphy.net/taxon_tcs.php?taxid=792

TCS seems to be really the XML standard to describe TaxonConcepts synonymy list entries.
The only open problem is how fine the granularity of a data set should be. I have now included any synonymy list of a distinct taxon in one TCS file. So our TCS granularity is at the taxon level. A finer granularity at he synonymy list level however also seems to be reasonable.

Dublin Core for Taxa

I recently wrote here that TaxonConcept will soon offer its metadata in TCS (Taxon Concept Schema) format to improve data exchange and interoperability with other groups. As the planned exchange interface will be a Open Archives (OAI) provider, we also have to deliver our data in Dublin Core (DC) format.
This brought up the problem how taxonomic data should be encoded in DC, which is mainly designed for document, electronic ressources and similar entities.
I had a short discussion with some of the members of the TDWG GUID list and decided to treat taxa similar to museum objects. For physical objects DC fields creator and date should contain e.g.the artist's name and date of creation instead of the name of the creator and publishing date of the electronic metadata representation. Therefore, I decided to use the creator tag for the taxon author, the date field as the date of description of the taxon and the title field for the taxon name. To describe the classification of a taxon I'll use the subject tag. Further, the relation tag will be used to handle the information TaxonConcepts stores from published synonymy lists.
An example:

<metadata>
<oai_dc:dc xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
<dc:format>text/html</dc:format>
<dc:format>application/pdf</dc:format>
<dc:rights>
Licensed under a Creative Commons Attribution 2.5 License
</dc:rights>
<dc:publisher>
Stratigraphy.Net http://taxonconcept.stratigraphy.net
</dc:publisher>
<dc:type>Taxon Concept</dc:type>
<dc:title>Eoglobigerina edita</dc:title>
<dc:date>1953</dc:date>
<dc:creator>Subbotina, N.N.</dc:creator>
<dc:identifier>
http://taxonconcept.stratigraphy.net/taxon_details.php?taxid=787
</dc:identifier>
<dc:relation>Globigerina edita Subbotina 1953</dc:relation>
<dc:relation>Globorotalia (Globorotalia) edita Subbotina 1953</dc:relation>
<dc:relation>Eoglobigerina edita edita Subbotina 1953</dc:relation>
<dc:relation>Globigerina edita var. polycamera Khalilov 1956</dc:relation>
<dc:relation>Eoglobigerina edita polycamera Khalilov 1956</dc:relation>
<dc:relation>
Globigerina (Eoglobigerina) hemisphaerica Morozova 1961
</dc:relation>
<dc:relation>
Globigerina (Eoglobigerina) tetragona Morozova 1961
</dc:relation>
<dc:relation>
Globigerina (Eoglobigerina) pentagona Morozova 1961
</dc:relation>
<dc:relation>
Globigerina (Eoglobigerina) theodosica Morozova 1961
</dc:relation>
<dc:relation>Globanomalina pentagona Morozova 1961</dc:relation>
<dc:subject>Eukaryota</dc:subject>
<dc:subject>Protoctista</dc:subject>
<dc:subject>Granuloreticulosa</dc:subject>
<dc:subject>Foraminifera</dc:subject>
<dc:subject>Globigerinida</dc:subject>
<dc:subject>Globigerinaceae</dc:subject>
<dc:subject>Globigerinidae</dc:subject>
<dc:subject>Eoglobigerinidae</dc:subject>
<dc:subject>Eoglobigerina</dc:subject>
<dc:subject>Eoglobigerina edita</dc:subject>
<dc:subject>Acarinina nitida</dc:subject>
</oai_dc:dc>
</metadata>

TaxonConcept's Taxon Concepts

Currently, TaxonConcept's data exchange capabilities are quite limited. This is mainly because we have not been able to determine a appropriate XML format which would allow us to represent the majority of TaxonConcepts information categories such as, concepts, descriptions, links to image objects, references etc.
Commonly used formats such as DarwinCore and ABCD are mainly designed to represent metadata of collection objects or species observation data and therefore not suited for our purposes. But at least TC's most important information pieces the taxonomic concepts and references can be represented fairly good by the TDWG standard TCS (TaxonConcept transfer schema).
According to this TDWG standard, a Taxon Concept is a name plus a description of a taxon, a definition which fits perfectly to what we do:
The taxonomic concepts stored in TC are entries of published synonymy lists. These basically represent definitions of individual taxonomic opinions by including or excluding other author's descriptions. In other words, a synonymy list is a Taxon Concept, which includes other Taxon Concepts.
The most difficult part when we start to translate our data to TCS will be the translation of 'Open Nomenclature' to TCS. Fortunately, TCS allows to represent our synonymy list entries as concept relationships, pro parte relationships (p) as well as misapplied names (non). which should enable us to create sufficient XML representations of our data.