[tdwg-content] Bioblitz as rdf: does this make sense?
Peter DeVries
pete.devries at gmail.com
Thu Jan 13 03:07:44 CET 2011
Hi Joel,
Cool :-)
I just loaded this into my SPARQL endpoint.
In the named graph urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz
It consists of 19,990 Triples
Here is one of the dwc:taxonConceptID entries.
*About: http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata*
http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata
*About: http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627*
<http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata>
http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627
<http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627>This
should give you an a count of occurrences.
SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#Occurrence>};
= 1882
SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#taxonConceptID>};
This should give you a list of occurrences
http://lsd.taxonconcept.org/describe/?url=http://rs.tdwg.org/dwc/terms/%23Occurrence
If this did not come through your email system try the bit.ly.
http://bit.ly/g9BcoL
I tried the following that should have given me a google map of all the
occurrences but it did not result in the map.
DESCRIBE ?x WHERE {
?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <
http://rs.tdwg.org/dwc/terms/#Occurrence>.
}
I looked that the RDF and I think I see the problem.
In the RDF
<geo:latitude>
41.53
</geo:latitude>
<geo:longitude>
-70.67
</geo:longitude>
Should be
<geo:lat>
41.53
</geo:lat>
<geo:long>
-70.67
</geo:long>
See http://www.w3.org/2003/01/geo/
I did the following query to get a list of all the dwc:taxonConceptID's and
have attached them as a .txt file.
select distinct ?o WHERE {?s <http://rs.tdwg.org/dwc/terms/#taxonConceptID>
?o}
Pretty neat :-)
There are some things that I will get back to Joel on.
Here is where you can manually enter a SPARQL query. Click on "Advanced" for
the entry window.
http://lsd.taxonconcept.org/isparql/
Respectfully,
- Pete
On Wed, Jan 12, 2011 at 5:55 PM, joel sachs <jsachs at csee.umbc.edu> wrote:
> Hi Everyone,
>
> I've posted rdf of the bioblitz data. It's at
> http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf .
>
> Individual occurrences can be retrieved via
> http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id]
> e.g. http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835
>
> Individual identifications can be retrieved via
> http://www.cs.umbc.edu/~jsachs/identifications/[identification_id]
> e.g.
> http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1
>
> The scripts behind this are on the kludgy side, so reports of errors and
> abnormalities will be warmly welcomed.
>
> Implicit in each of the following notes is the question "Is this a good
> way to do it?":
>
> 1. The data is "normalized" w.r.t. identification. "Normalized" is in
> quotes because I mean it in the sense that Steve Baskauf was using in his
> Fall 2010 series of posts. His meaning of the term makes sense to me, but
> many people (e.g. the OBO folks), take "normalized ontology" to mean
> "disentangled" (i.e. no multiple inheritance.)
> As an example, here's an occurrence with two crowdsourced determinations:
> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644
>
> 2. I used sequential integers for observation and identification IDs; in
> practice, a mechanism needs to be in place to prevent two people from
> assigning the same id to their respective identifications.
>
> 3. My answer to Cam Webb's Question #1 from
> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html
> is "both". In other words, just as "Joel Sachs" is both me and also my
> name, so
> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668 is both
> an occurrence and an occurrence_id, expressed as:
> ---
> <dwc:Occurrence
> rdf:about="
> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644">
> <dwc:occurrenceID>
> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644
> </dwc:occurrenceID>
> <blah blah blah/>
> </dwc:Occurrence>
> ---
>
> 4. I was surprised to see that the Darwin Core Identification class has no
> "occurrenceID" or "specimenID" term. How is one supposed to tie an
> identification to an observation (assuming the identification is not
> in-lined, of course)? DeVries and Baskauf each mint their own terms for
> doing this (txn:identificationHasOccurrence, and sernec:basedOnOccurrence,
> respectively); I used dwc:occurrenceID as if it were a record level term.
>
> 5. We had scope for multiple taxonConceptID columns in the Fusion table,
> and assigned lsids where possible. I also mean to work with Pete to assign
> GUIDs from taxoncocept.org. In addition, I assigned ethan taxon concept
> ids, which look like this:
> http:.//spire.umbc.edu/ethan/Coffea_arabica
>
> In their argument over opaque vs. transparent taxonCoceptIDs, I was
> sympathetic to both Pete's and Gregor's arguments. Ultimately, if the
> tooling exists to always display the rdfs:labels every time I'm loooking
> at a list of opaqueIDs, then transparent IDs are unnecessary. But, for
> now, it's really helpful to look at an ID and know what it's referring to.
>
> (For species names not in the spire database, the rdf returned by
> http:.//spire.umbc.edu/ethan/$name
> is simply an rdfs:seeAlso to
> http://http://gni.globalnames.org/name_strings?search_term=$name)
>
> 6. It was easy to assert membership in RDF classes corresponding to
> various Cape Cod categories of concern - invasive species, threatenened
> species, indicators, etc. You can see these classes at
> http://spire.umbc.edu/ontologies/lists (Information of where these lists
> come from is included as rdfs:comments. I'll add further documentation,
> e.g. links to eml files.)
>
> Note that "ThingOfConcern" is defined as the superclass of all the other
> classes in the collection. The idea here is that people can create their
> own "ThingOfConcern" class, and then query for observations that are of
> concern to them. You can see sample sparql queries at
> http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt
>
>
> As an aside, I think we, as a community, should come up with a
> biodiversity benchmark suite of rdf data and corresponding sparql queries,
> that can be
> used to test the suitability and scalability of semantic web knowledge
> bases. I'll take this up in a future post (unless someone beats me to it).
>
> Comments, questions, and better ideas are welcome.
>
> Thanks -
> Joel.
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
--
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies
Knowledge Base <http://lod.geospecies.org/>
About the GeoSpecies Knowledge Base <http://about.geospecies.org/>
------------------------------------------------------------
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http://spire.umbc.edu/ethan/Bartonia_virginica
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http://spire.umbc.edu/ethan/Bidens_frondosa
http://spire.umbc.edu/ethan/Blattodea
http://spire.umbc.edu/ethan/Boletus_bicolor
http://spire.umbc.edu/ethan/Bombus
http://spire.umbc.edu/ethan/Bombus_abnormis
http://spire.umbc.edu/ethan/Bombus_impatiens
http://spire.umbc.edu/ethan/Botrylloides
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http://spire.umbc.edu/ethan/Chamaedaphne_caliculata
http://spire.umbc.edu/ethan/Champia_parvula
http://spire.umbc.edu/ethan/Chenopodium
http://spire.umbc.edu/ethan/chicoreum_intybus
http://spire.umbc.edu/ethan/Chilopoda
http://spire.umbc.edu/ethan/Chimaphila_maculata
http://spire.umbc.edu/ethan/Chimaphilla_maculata
http://spire.umbc.edu/ethan/Chimaphilla_umbellata
http://spire.umbc.edu/ethan/Chondrus_crispus
http://spire.umbc.edu/ethan/Cichorium_intybus
http://spire.umbc.edu/ethan/Cicindella_sexguttata
http://spire.umbc.edu/ethan/Ciona_intestinalis
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http://spire.umbc.edu/ethan/Cladonia
http://spire.umbc.edu/ethan/Clematis_sp.
http://spire.umbc.edu/ethan/Clematis_spp.
http://spire.umbc.edu/ethan/Clethra_almiflora
http://spire.umbc.edu/ethan/Clethra_alnifolia
http://spire.umbc.edu/ethan/Coccotylus_truncatus
http://spire.umbc.edu/ethan/Codium
http://spire.umbc.edu/ethan/Codium_fragile
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http://spire.umbc.edu/ethan/Colinus_virginianus
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http://spire.umbc.edu/ethan/commalina_communis
http://spire.umbc.edu/ethan/Commelina
http://spire.umbc.edu/ethan/Commelina_communis
http://spire.umbc.edu/ethan/Comptonia_peregrina
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http://spire.umbc.edu/ethan/Coprinus_truncorum
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http://spire.umbc.edu/ethan/Coronilla_varia
http://spire.umbc.edu/ethan/Cortinarius_alboviolaceus
http://spire.umbc.edu/ethan/Cortinarius_alboviolaceus_(Pers.)_Fr._1838
http://spire.umbc.edu/ethan/Cortinarius_corrugatus
http://spire.umbc.edu/ethan/Cortinarius_iodes
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http://spire.umbc.edu/ethan/Cortinarius_semisanguineus_(Fr.)_Gillet_1874
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http://spire.umbc.edu/ethan/Cyperus_Esculantus
http://spire.umbc.edu/ethan/Cyperus_esculentus
http://spire.umbc.edu/ethan/Cyperus_esculentus_L.
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http://spire.umbc.edu/ethan/Cyprinodon_variegatus
http://spire.umbc.edu/ethan/Cypripedium_acaule
http://spire.umbc.edu/ethan/Cypripedium_sp.
http://spire.umbc.edu/ethan/Cyrpepedium_acaule
http://spire.umbc.edu/ethan/Dasya_pedicellata
http://spire.umbc.edu/ethan/Daucus_carota
http://spire.umbc.edu/ethan/Daucus_carota_L.
http://spire.umbc.edu/ethan/Decodon_verticillatus
http://spire.umbc.edu/ethan/Dendroica_coronata
http://spire.umbc.edu/ethan/Dendroica_palmarum
http://spire.umbc.edu/ethan/Dendroica_petechia_(Linnaeus,_1766)
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http://spire.umbc.edu/ethan/Desmodium_paniculatum
http://spire.umbc.edu/ethan/Desmodium_sp.
http://spire.umbc.edu/ethan/Dichanthelium_sp.
http://spire.umbc.edu/ethan/Dicranium_sp
http://spire.umbc.edu/ethan/Dicranum_bonjeanii
http://spire.umbc.edu/ethan/Dicranum_scoparia
http://spire.umbc.edu/ethan/Dicranum_scoparium
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http://spire.umbc.edu/ethan/Didemnum_albidum
http://spire.umbc.edu/ethan/Digitaria_sanguinalis_(L.)_Scop.
http://spire.umbc.edu/ethan/Diplopoda
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http://spire.umbc.edu/ethan/Dumetella_carolinensis
http://spire.umbc.edu/ethan/Dumetella_carolinensis_(Linnaeus,_1766)
http://spire.umbc.edu/ethan/Ectocarpales
http://spire.umbc.edu/ethan/Edwardsiella
http://spire.umbc.edu/ethan/Eichhornia_crassipes
http://spire.umbc.edu/ethan/Elaeagnus_umbellata
http://spire.umbc.edu/ethan/Eleagnus_umbellata
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http://spire.umbc.edu/ethan/Epigea_repens
http://spire.umbc.edu/ethan/Eragraostis_speckililis
http://spire.umbc.edu/ethan/Eragrostis_spectabilis
http://spire.umbc.edu/ethan/Eriophorum_sp.
http://spire.umbc.edu/ethan/Eucosma_dorsisignatana
http://spire.umbc.edu/ethan/Euonymus
http://spire.umbc.edu/ethan/Eupatorium_hyssopifolium
http://spire.umbc.edu/ethan/Eupatorium_perfoliatum_L.
http://spire.umbc.edu/ethan/Eupatorium_prefoliatum
http://spire.umbc.edu/ethan/Eupatorium_Prefoliatum
http://spire.umbc.edu/ethan/Euphorbia_maculata_L.
http://spire.umbc.edu/ethan/Euthamia_graminafolia
http://spire.umbc.edu/ethan/Euthamia_Graminifolia
http://spire.umbc.edu/ethan/Euthamia_graminifolia_(L.)_Nutt.
http://spire.umbc.edu/ethan/Euthamia_tenuifolia
http://spire.umbc.edu/ethan/Euthamia_Tenuifolia
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http://spire.umbc.edu/ethan/Lonicera_morowii
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http://spire.umbc.edu/ethan/Lycopodium_sp,
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http://spire.umbc.edu/ethan/Mytilus_edulis
http://spire.umbc.edu/ethan/Nomophila_nearctica
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http://spire.umbc.edu/ethan/Nyssa_sylvatica
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http://spire.umbc.edu/ethan/Ocadia_glyphistoma
http://spire.umbc.edu/ethan/Oceanites_oceanicus
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http://spire.umbc.edu/ethan/Opiliones
http://spire.umbc.edu/ethan/Orbicularia_auricolor
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http://spire.umbc.edu/ethan/Oxalis_sp.
http://spire.umbc.edu/ethan/pandion_haliaetus
http://spire.umbc.edu/ethan/Pandion_haliaetus
http://spire.umbc.edu/ethan/Panellus_stypticus
http://spire.umbc.edu/ethan/Panicum_caldestinum
http://spire.umbc.edu/ethan/Panicum_clandestinum
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http://spire.umbc.edu/ethan/Queras_alba
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http://spire.umbc.edu/ethan/Solidago_puberula
http://spire.umbc.edu/ethan/Solidago_rugosa
http://spire.umbc.edu/ethan/Solidago_Semfer
http://spire.umbc.edu/ethan/Solidago_sempervirens
http://spire.umbc.edu/ethan/Solidago_Sempervirens
http://spire.umbc.edu/ethan/Solidago_sempervirens_L.
http://spire.umbc.edu/ethan/Solidago_uliginosa_Nutt.
http://spire.umbc.edu/ethan/Solticidae
http://spire.umbc.edu/ethan/Somateria_mollissima
http://spire.umbc.edu/ethan/Spartina
http://spire.umbc.edu/ethan/Spartina_alterniflora
http://spire.umbc.edu/ethan/Spartina_alterniflora_Loisel.
http://spire.umbc.edu/ethan/Spartina_patens
http://spire.umbc.edu/ethan/Spartina_pectinata_Bosc_ex_Link
http://spire.umbc.edu/ethan/Spartina_Pectineta
http://spire.umbc.edu/ethan/Spergularia_marina
http://spire.umbc.edu/ethan/Sphagnum
http://spire.umbc.edu/ethan/Sphagnum_fimbriata_s.l.
http://spire.umbc.edu/ethan/Sphagnum_papillatum_s.l.
http://spire.umbc.edu/ethan/Sphagnum_sp.
http://spire.umbc.edu/ethan/Spiraea
http://spire.umbc.edu/ethan/Spirobus_borealis
http://spire.umbc.edu/ethan/Spirobus_spp
http://spire.umbc.edu/ethan/Spizella_passerina
http://spire.umbc.edu/ethan/Spodoptera_frugiperda
http://spire.umbc.edu/ethan/Stercorarius_parasiticus
http://spire.umbc.edu/ethan/Stereum_complicatum
http://spire.umbc.edu/ethan/Stereum_ostrea
http://spire.umbc.edu/ethan/Sterna_paradisaea
http://spire.umbc.edu/ethan/Strobilomyces_confusus
http://spire.umbc.edu/ethan/Strobilomyces_floccopus
http://spire.umbc.edu/ethan/Strobilomyces_strobilaceus_(Scop.)_Berk._1860
http://spire.umbc.edu/ethan/Sturnus_argentus
http://spire.umbc.edu/ethan/Sturnus_vulgaris_Linnaeus_1758
http://spire.umbc.edu/ethan/Styela_clava
http://spire.umbc.edu/ethan/Suaeda_sp1
http://spire.umbc.edu/ethan/Suaeda_sp2
http://spire.umbc.edu/ethan/Suillus_salmonicolor
http://spire.umbc.edu/ethan/Sulus_bassanus
http://spire.umbc.edu/ethan/Sunira_bicolorago
http://spire.umbc.edu/ethan/Sympetrum_vicinum
http://spire.umbc.edu/ethan/Symphiotricum_dumosum
http://spire.umbc.edu/ethan/Symphyotrichum_dumosum
http://spire.umbc.edu/ethan/Symphyotrichum_ericoides
http://spire.umbc.edu/ethan/Symphyotrichum_laeve
http://spire.umbc.edu/ethan/Symphyotrichum_linearifolium
http://spire.umbc.edu/ethan/Symphyotrichum_pilosum_(Willd.)_G._L._Nesom
http://spire.umbc.edu/ethan/Tachycineta_bicolor
http://spire.umbc.edu/ethan/Tachycineta_bicolor_(Vieillot,_1808)
http://spire.umbc.edu/ethan/Tapinella_atrotomentosa
http://spire.umbc.edu/ethan/Tefanolita_mynesalis
http://spire.umbc.edu/ethan/Tetramorium_caespitum
http://spire.umbc.edu/ethan/The_Blob.
http://spire.umbc.edu/ethan/Thelypteris_sp.
http://spire.umbc.edu/ethan/Theridiidae
http://spire.umbc.edu/ethan/Thomisidae
http://spire.umbc.edu/ethan/Thryothorus_ludovicianus
http://spire.umbc.edu/ethan/Thryothorus_ludovicianus_(Latham,_1790)
http://spire.umbc.edu/ethan/Thunnus_thynnus
http://spire.umbc.edu/ethan/Thysanoptera
http://spire.umbc.edu/ethan/Toxicodendron_diversilobum
http://spire.umbc.edu/ethan/Toxicodendron_radicans
http://spire.umbc.edu/ethan/Toxicodendron_radicans_(L.)_Kuntze
http://spire.umbc.edu/ethan/Toxomerus_marginatus
http://spire.umbc.edu/ethan/Trametes_pubescens
http://spire.umbc.edu/ethan/Trametes_versicolor
http://spire.umbc.edu/ethan/Triadenum_virginianum
http://spire.umbc.edu/ethan/Trichaptum_biforme
http://spire.umbc.edu/ethan/Trichoglossum_walteri
http://spire.umbc.edu/ethan/Tricholoma_caligatum
http://spire.umbc.edu/ethan/Tricholoma_davisiae
http://spire.umbc.edu/ethan/Trientalis_borealis
http://spire.umbc.edu/ethan/Trifolium_repens
http://spire.umbc.edu/ethan/Trifolium_repens_L.
http://spire.umbc.edu/ethan/Turdus_migratorius
http://spire.umbc.edu/ethan/Turdus_migratorius_Linnaeus_1766
http://spire.umbc.edu/ethan/Tylopilus_ballouii
http://spire.umbc.edu/ethan/Tylopilus_chromipes
http://spire.umbc.edu/ethan/Tylopilus_felleus
http://spire.umbc.edu/ethan/Typha_latifolia
http://spire.umbc.edu/ethan/Uca_Pugnax
http://spire.umbc.edu/ethan/Udea_rubigalis
http://spire.umbc.edu/ethan/Ulmus_pumila
http://spire.umbc.edu/ethan/Ulva
http://spire.umbc.edu/ethan/Ulva_intestinalis
http://spire.umbc.edu/ethan/urosalpinx_cinerea
http://spire.umbc.edu/ethan/Usnea_sp.
http://spire.umbc.edu/ethan/Ustialgo_syntherismae
http://spire.umbc.edu/ethan/Vaccinium_angustifolium
http://spire.umbc.edu/ethan/Vaccinium_corymbosum
http://spire.umbc.edu/ethan/Vaccinium_corymbosum_L.
http://spire.umbc.edu/ethan/Vaccinium_macrocarpus
http://spire.umbc.edu/ethan/Vaccinium_pallidum
http://spire.umbc.edu/ethan/Verbascum_thapsus
http://spire.umbc.edu/ethan/Vibarnum_dentatum
http://spire.umbc.edu/ethan/Vibernum_dentatum
http://spire.umbc.edu/ethan/Vibernum_nudum
http://spire.umbc.edu/ethan/Vibirum_dentatum
http://spire.umbc.edu/ethan/Viburnum_dentatum
http://spire.umbc.edu/ethan/Viburnum_nudum
http://spire.umbc.edu/ethan/Vicia_sp.
http://spire.umbc.edu/ethan/Vitis_aestivalis_Michx.
http://spire.umbc.edu/ethan/Vitis_sp.
http://spire.umbc.edu/ethan/Woodwardia_areolata
http://spire.umbc.edu/ethan/Woodwardia_virginica
http://spire.umbc.edu/ethan/Xanthoria_elegans
http://spire.umbc.edu/ethan/Xestia_dilucida
http://spire.umbc.edu/ethan/yellow_flower
http://spire.umbc.edu/ethan/Zanclognatha_marcidelinea
http://spire.umbc.edu/ethan/Zanclognatha_marcidilinea
http://spire.umbc.edu/ethan/Zostera
http://spire.umbc.edu/ethan/Zostera_marina
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