tdwg-rdf - DataInventory.wiki

Contents

Introduction

In response to Rod Page's challenge, in follow-up to discussions on creating a biodiversity RDF sandbox, and in furtherance of our mission, we will load as much biodiversity data as we can into a triplestore. We'll use this page to inventory the data we probably want to include. Where possible, include links to rdf representations of the data (data dumps, sparql endpoints, etc.)

Biodiversity RDF datasets and other semantic web infrastructure

taxonconcept.org http://www.taxonconcept.org/sparql-endpoint/ This SPARQL endpoint has 23 million triples and includes some other related databases. Queries can be done directly on that endpoint at http://lsd.taxonconcept.org/sparql for a generic web interface and at http://lsd.taxonconcept.org/isparql for a human-friendly interface. Datasets include the Global Name Index (GNI), DBpedia, geonames, etc. in addition to Pete's taxonconcept.org database.
Natural Solutions virtuoso triple store: so far we have put in Rod's datasets on frogs. http://82.96.149.133:8890/sparql Feel Free to play with the SPARQL interface.

Specimens at Royal Botanic Garden Edinburgh

Described in Hyam, R.D., Drinkwater, R.E. & Harris, D.J. Stable citations for herbarium specimens on the internet: an illustration from a taxonomic revision of Duboscia (Malvaceae) Phytotaxa 73: 17–30 (2012). http://www.mapress.com/phytotaxa/content/2012/f/pt00073p030.pdf

Example resource: http://data.rbge.org.uk/herb/E00435912 which dereferences to a web page or RDF/XML via a 303 redirect.

RDF/XML: ```

Simple PHP RDF Script 2013-11-10T01:46:58+00:00

Goldsmith, M. #207 Duboscia macrocarpa Bocq. A herbarium specimen of Duboscia macrocarpa Bocq. collected by Goldsmith, M. #207 Goldsmith, M. 1973

--> 2.866667 16.466667 -->

http://data.rbge.org.uk/herb/E00435912 2011-08-19 00:00:00 Specimen http://biocol.org/urn:lsid:biocol.org:col:15670 E E00435912 Duboscia macrocarpa Bocq. Malvaceae Duboscia macrocarpa Tropical Africa CF Sangha-Mbaere Bai Hoku. 16.466667 2.866667 1973 Goldsmith, M. image/jpegImage of herbarium specimen2011-08-22T11:38:48Z

```

RDF/Turtle: ``` @prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#. @prefix rdfs: http://www.w3.org/2000/01/rdf-schema#. @prefix xsd: http://www.w3.org/2001/XMLSchema#. @prefix xsi: http://www.w3.org/2001/XMLSchema-instance. @prefix tap: http://rs.tdwg.org/tapir/1.0. @prefix xs: http://www.w3.org/2001/XMLSchema. @prefix hyam: http://hyam.net/tapir2sw#. @prefix dwc: http://rs.tdwg.org/dwc/terms/. @prefix dwcc: http://rs.tdwg.org/dwc/curatorial/. @prefix dc: http://purl.org/dc/terms/. @prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos#.

http://data.rbge.org.uk/herb/E00435912 dc:created "1973"; dc:creator "Goldsmith, M."; dc:description "A herbarium specimen of Duboscia macrocarpa Bocq. collected by Goldsmith, M. #207 "; dc:modified "2011-08-19 00:00:00"; dc:relation http://data.rbge.org.uk/images/393342; dc:title "Goldsmith, M. #207 Duboscia macrocarpa Bocq."; dwc:BasisOfRecord "Specimen"; dwc:CatalogNumber "E00435912"; dwc:CollectionCode "E"; dwc:Collector "Goldsmith, M."; dwc:Country "CF"; dwc:DecimalLatitude "2.866667"; dwc:DecimalLongitude "16.466667"; dwc:EarliestDateCollected "1973"; dwc:Family "Malvaceae"; dwc:Genus "Duboscia"; dwc:HigherGeography "Tropical Africa"; dwc:InstitutionCode "http://biocol.org/urn:lsid:biocol.org:col:15670"; dwc:Locality "Bai Hoku."; dwc:SampleID "http://data.rbge.org.uk/herb/E00435912"; dwc:ScientificName "Duboscia macrocarpa Bocq."; dwc:SpecificEpithet "macrocarpa"; dwc:StateProvince "Sangha-Mbaere"; geo:lat "2.866667"; geo:long "16.466667". http://data.rbge.org.uk/images/393342 dc:created "2011-08-22T11:38:48Z"; dc:description "Image of herbarium specimen"@en; dc:format "image/jpeg"; dc:identifier http://data.rbge.org.uk/images/393342; dc:subject http://data.rbge.org.uk/herb/E00435912; dc:type http://purl.org/dc/dcmitype/Image. http://data.rbge.org.uk/service/rdf/herb.php?guid=http://data.rbge.org.uk/herb/E00435912 dc:created "2013-11-10T01:46:58+00:00"; dc:creator "Simple PHP RDF Script"; dc:hasVersion http://elmer.rbge.org.uk/bgbase/vherb/bgbasevherb.php?cfg=bgbase/vherb/fulldetails.cfg%26amp;specimens_specimen__num=E00435912. ``` Note: this RDF uses a bit of fanciful Darwin Core (incorrect case, dwc:Collector, etc.)

Specimens in ARCTOS/University of Alaska Museum of the North

HTTP URIs for specimens such as http://arctos.database.museum/guid/UAM:Ento:230092 which is the same for all specimens in the ARCTOS system. However, UA Museum of the North also uses DOIs such as http://dx.doi.org/10.7299/X7VQ32SJ which redirect in a browser to the same web page as the ARCTOS HTTP URI.

Dereferencing the DOI requesting RDF/XML gets: <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:j.0="http://purl.org/dc/terms/" > <rdf:Description rdf:about="http://dx.doi.org/10.7299/X7VQ32SJ"> <j.0:creator>Derek S. Sikes</j.0:creator> <j.0:publisher>University of Alaska Museum</j.0:publisher> <j.0:title>UAM:Ento:230092 - Grylloblatta campodeiformis</j.0:title> <j.0:date>2004</j.0:date> <owl:sameAs>doi:10.7299/X7VQ32SJ</owl:sameAs> <owl:sameAs>info:doi/10.7299/X7VQ32SJ</owl:sameAs> <j.0:identifier>10.7299/X7VQ32SJ</j.0:identifier> </rdf:Description> </rdf:RDF>

http://dx.doi.org/10.7299/X7VQ32SJ http://purl.org/dc/terms/creator "Derek S. Sikes"; http://purl.org/dc/terms/date "2004"; http://purl.org/dc/terms/identifier "10.7299/X7VQ32SJ"; http://purl.org/dc/terms/publisher "University of Alaska Museum"; http://purl.org/dc/terms/title "UAM:Ento:230092 - Grylloblatta campodeiformis"; owl:sameAs "doi:10.7299/X7VQ32SJ", "info:doi/10.7299/X7VQ32SJ". ```

Dereferencing the HTTP URI requesting RDF/XML gets this file (which has some validation problems): ``` http://arctos.database.museum/contact.cfm We'd love to hear your feedback. Or just tell us you found this thing.

This document in no way represents all information available from Arctos. --> Sayde Ridling 2012-11-29 UAM:Ento:230092 - UAM Insects 230092 Grylloblatta campodeiformis UAM Insects 230092 Grylloblatta campodeiformis 50.8657666667 -115.2110333333 2013-09-18 http://arctos.database.museum/guid/UAM:Ento:230092 PreservedSpecimen UAM Ento 230092 Grylloblatta campodeiformis Animalia Arthropoda Insecta Gryllablattodea Grylloblattidae Grylloblatta campodeiformis Walker 1914 Arthropoda Insecta Gryllablattodea Grylloblattidae Grylloblatta Grylloblatta campodeiformis Karl J. Jarvis North America, Canada, Alberta North America Canada Alberta Kananaskis. Galatca, trail to Lilian Lake N of Rt. 40 S of Kananaskis Village 50.8657666667 -115.2110333333 World Geodetic System 1984 degrees dec. minutes 50d 51.946m N/115d 12.662m W Field GPS Unit MaNIS georeferencing guidelines 10 1761.744 1798.32 5780-5900 ft voucher of Grylloblatta campodeiformis Walker 1914, page 227 in Jarvis %26amp; Whiting 2006 female vial (100% ethanol) whole organism 1 adult GenBank=DQ457228; GenBank=DQ457263; GenBank=DQ457300; secondary identifier=BYU_gb32.1 http://www.ncbi.nlm.nih.gov/nuccore/DQ457228; http://www.ncbi.nlm.nih.gov/nuccore/DQ457263; http://www.ncbi.nlm.nih.gov/nuccore/DQ457300 Derek S. Sikes 2004-10-09 2004-10-09 9 Oct 2004 DNA Holotype GB 32.1 left side mid and hind legs removed for molecular data, hind leg in vial with specimen. http://arctos.database.museum/MediaSearch.cfm?action=search%26amp;media_id=10322363,10322362 ```

In RDF/Turtle (after fixing invalid RDF): ``` @prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#. @prefix rdfs: http://www.w3.org/2000/01/rdf-schema#. @prefix xsd: http://www.w3.org/2001/XMLSchema#. @prefix xsi: http://www.w3.org/2001/XMLSchema-instance. @prefix tap: http://rs.tdwg.org/tapir/1.0. @prefix xs: http://www.w3.org/2001/XMLSchema. @prefix hyam: http://hyam.net/tapir2sw#. @prefix dwc: http://rs.tdwg.org/dwc/terms/. @prefix dwcc: http://rs.tdwg.org/dwc/curatorial/. @prefix dc: http://purl.org/dc/terms/. @prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos#.

http://arctos.database.museum/guid/UAM:Ento:230092 dc:created "2012-11-29"; dc:creator "Sayde Ridling"; dc:description "UAM Insects 230092 Grylloblatta campodeiformis"; dc:hasVersion http://arctos.database.museum/guid/UAM:Ento:230092; dc:modified "2013-09-18"; dc:title "UAM:Ento:230092 - UAM Insects 230092 Grylloblatta campodeiformis"; dwc:AgeClass "adult "; dwc:BasisOfRecord "PreservedSpecimen"; dwc:CatalogNumber "230092"; dwc:Class "Insecta"; dwc:CollectionCode "Ento"; dwc:Collector "Derek S. Sikes"; dwc:ContinentOcean "North America"; dwc:CoordinateUncertaintyInMeters "10"; dwc:Country "Canada"; dwc:County ""; dwc:DecimalLatitude "-115.2110333333"; dwc:DecimalLongitude "50.8657666667"; dwc:EarliestDateCollected "2004-10-09"; dwc:Family "Grylloblattidae"; dwc:GenBankNum "http://www.ncbi.nlm.nih.gov/nuccore/DQ457228; http://www.ncbi.nlm.nih.gov/nuccore/DQ457263; http://www.ncbi.nlm.nih.gov/nuccore/DQ457300"; dwc:Genus "Grylloblatta"; dwc:GeoreferenceProtocol "MaNIS georeferencing guidelines"; dwc:GeoreferenceSource "Field GPS Unit"; dwc:HigherGeography "North America, Canada, Alberta"; dwc:HigherTaxon "Animalia Arthropoda Insecta Gryllablattodea Grylloblattidae Grylloblatta campodeiformis Walker 1914"; dwc:HorizontalDatum "World Geodetic System 1984"; dwc:IdentifiedBy "Karl J. Jarvis"; dwc:ImageURL "http://arctos.database.museum/MediaSearch.cfm?action=search%26amp;media_id=10322363,10322362"; dwc:IndividualCount "1"; dwc:InstitutionCode "UAM"; dwc:Island ""; dwc:IslandGroup ""; dwc:Kingdom ""; dwc:LatestDateCollected "2004-10-09"; dwc:Locality "Kananaskis. Galatca, trail to Lilian Lake N of Rt. 40 S of Kananaskis Village"; dwc:MaximumDepthInMeters ""; dwc:MaximumElevationInMeters "1798.32"; dwc:MinimumDepthInMeters ""; dwc:MinimumElevationInMeters "1761.744"; dwc:Order "Gryllablattodea"; dwc:OriginalCoordinateSystem "degrees dec. minutes"; dwc:OtherCatalogNumbers "GenBank=DQ457228; GenBank=DQ457263; GenBank=DQ457300; secondary identifier=BYU_gb32.1"; dwc:Phylum "Arthropoda"; dwc:Preparations "vial (100% ethanol) whole organism"; dwc:RelatedCatalogedItems ""; dwc:Remarks "DNA Holotype GB 32.1 left side mid and hind legs removed for molecular data, hind leg in vial with specimen."; dwc:SampleID "http://arctos.database.museum/guid/UAM:Ento:230092"; dwc:ScientificName "Grylloblatta campodeiformis"; dwc:Sex "female "; dwc:Species "Grylloblatta campodeiformis"; dwc:StateProvince "Alberta"; dwc:Subspecies ""; dwc:TypeStatus "voucher of Grylloblatta campodeiformis Walker 1914, page 227 in Jarvis %26amp; Whiting 2006"; dwc:VerbatimCollectingDate "9 Oct 2004"; dwc:VerbatimCoordinates "50d 51.946m N/115d 12.662m W"; dwc:VerbatimElevation "5780-5900 ft"; geo:lat "50.8657666667"; geo:long "-115.2110333333". ``` Also contains some non-standard Darwin Core (incorrect case, dwc:Collector, dwc:AgeClass, etc.)

Specimen in Linked Open Data Of Ecology

Example HTTP URI: http://ecowlim.tfri.gov.tw/lode/resource/flyhorse/Specimen/5023

Dereferences in a browser showing results of a SPARQL query. Dereferences as RDF/XML through 303 redirect.

In RDF/XML: ``` RDF description of Flyhorse DB Insect Specimen #5023 http://fact.tfri.gov.tw/smec/TFRI/m_images/00013880.jpg W. Hwang 黃文伯

0 Taiwan 張玉珍 Flyhorse DB Insect Specimen #5023 Yangmingshan 中華民國台灣 Y. C. Chang Taipei City 陽明山 5023 台北市 TC13 TC ```