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@%META:TOPICINFO{author="BobMorris" date="1263787732" format="1.1" reprev="1.58" version="1.58"}%
%META:TOPICPARENT{name="WebHome"}%
[[http://plazi.org Plazi]] is a non-profit organization dedicated to advancing open scientific literature. Its main project at the moment is the development of tools for automation of extraction of information from publications, whether scanned or born digital, and web services for applying and providing such information. This page is discusses an effort underway to use SPM to serve species descriptions, and related data from systematics literature. The work is funded by the Encyclopedia of Life and administered by GBIF and carried out for [[http://plazi.org Plazi]] by Main.TerryCatapano and Main.BobMorris. It builds on work originally funded by the U.S. National Science Foundation at the American Museum of Natural History and the University of Massachusetts/Boston.
This is a complete rewrite and synthesis reflecting our understanding as of Oct 10 2008 and onward. It addresses remarks, answers, and questions made in earlier versions by Main.RogerHyam and Main.PatrickLeary and ourselves, including some simple things we were doing wrong. As of Jan 22, 2009 and onward, all the issues raised in earlier versions of this page have been addressed and the service described below is complete, subject only to some tuning. The discussion leading to it can be found by examining the history, and is also frozen at PlaziSPMDiscussion. Thanks to Roger and Patrick for their comments.
The actual RDF vocabularies at issue can be found at [[http://rs.tdwg.org/ontology/voc/SpeciesProfileModel.rdf]] and [[http://rs.tdwg.org/ontology/voc/SPMInfoItems.rdf]]
%TOC%
---+Plazi Report To GBIF and EOL
PlaziFinalReport
---+Plazi SPM REST service
As of 22 January, we offer a REST service requiring the user to choose one of two serializations, described below. The full api for the REST service follows those descriptions. In all cases, the document is returned as RDF/XML conforming to the definition of SPM. The API described below controls the content and rendering format of the spm:hasContent elements, which is what most clients will be inserting into their applications.
Base URL:
http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/getSPM.xq
Required Parameters:
* &doc=[document name] This parameter sets the document to be retrieved as SPM
* Use one of each pair of following parameters:
* &description:
* &description=narrow This parameter imposes a narrow view of what consitutes an spmi:Description. It extracts from a publication only the classical description, i.e. the characters and states that describe the taxon under consideration, for insertion into the appropriate spm:hasContent element.
* &description=broad This parameter imposes a broad view of an spmi:Description. Application of it in the REST service results in all of the sections of a treatment returned, e.g. _materials examined_, _description_, _diagnosis_, _etymology_, etc., separated from one another in ways that identify them. These appear in the appropriate spm:hasContent element. For future work we will propose a controlled vocabulary for these parts of a treatment so that they can be marked up more explicitly in RDF.
* &render:
* &render=text The spm:hasContent items are plain text, with paragraphs separated by white space.
* &render=xhtml The spm:hasContent items are xhtml with character entities require escaping. This rendering will require that a client filters the escaped entities, particularly the xhtml escaped brackets, to turn it into xhtml suitable for browsers.
* &associations:
* &associations=yes For each taxon name appearing in the treatment of the described taxon an spm:associatedTaxon is created inside an spmi:Associations
* &associations=no No information about associated taxa is returned
Other changes
* added dc:rights with string "Not copyrightable" added to spm:SpeciesProfileModel
* added an spm:associatedTaxon for each taxon name in the treatment serving as source of each spm:SpeciesProfileModel
* added xml comments for revision number of xsl stylesheet converting from taxonX to SPM and timestamp for date and time of transformation
---+ Generally Current Example
Click below for an example generated by the current, live SPM server. Many browsers do not reveal the tags in RDF/XML, so you may have to do "View Source" in your browser to see them.
[[http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=narrow][http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=broad&associations=no]]
Click below to query the service and invoke the w3c RDF validator against the result, showing the rdf triples and graph.
[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=broad&associations=no&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][Click for RDF validation, triples and graph from the W3C online RDF validator]]
The text example below might not be completely up to date. In a comment near the top of it, the RDF will carry the date of its construction and the date and version of the underlying XSLT that produced the SPM RDF. This is current as of the "Generated" date
Donisthorpe, H. S. J. K.
A new Camponotus from Madagascar and a small collection of ants from Mauritius.
Annals and Magazine of Natural History
(12)2
1949
271-275
Camponotus gerberti
Species
Public domain.
[[ soldier ]]. Very pale dirty yellow, head reddish yellow, mandibles dark red, teeth, scapes, anterior border of clypeus, and extreme anterior angles of cheeks black, clothed with very sparse outstanding longer and shorter yellow hairs and some fine very short decumbent yellow hairs. Sculpture consisting of very fine reticulations, a little stronger on head.
Head large, triangular, considerably broader behind than in front, broadest a little before posterior angles, which are rounded and prominent, posterior border excised, slightly sinuate on each side; mandibles massive, strongly punctured and with transverse ridges, masticatory border armed with six large strong teeth, the apical one being the longest, curved and sharp, the next two longer and sharper than the last three; clypeus large, somewhat flat, carinate and slightly convex on disc, anterior border considerably produced in middle where it is somewhat crenulate, and five large punctures are present along the edge, and smaller punctures, rather wide apart, are scattered over the rest of the surface, posterior border excised in middle; frontal area very faintly defined; frontal carinas rather long, raised, with sharp edges, the rims or edges enclosing the antennal sockets are considerably raised and prominent; a very fine narrow longitudinal ridge takes the place of the frontal furrow and extends between the frontal carinae as far back as their extreme edges; eyes large, broad oval, rather flat, are situated rather high up before the middle of the sides of the head; antenna 12 - jointcd, scape long, thickened at apex, extending beyond the posterior border of head funiculus with all the joints elongate, first slightly shorter than the others, last joint long and pointed. Thorax longer than broad, broadest behind centre of sides of pronotum, somewhat slender behind; pronotum ample. convex, with a short neck, sides margined, considerably widened afterneck, posterior border semicircular; sutures between pro- and mesonotum, and meso- and epinotum fine but distinct; mesonotum longer than broad, shorter than pronotum, somewhat flat on disc, sides rather straight, epinotum longer than mesonotum, sides rather straight, angle between dorsal surface and declivity not marked, dorsal surface longer than declivity. Scale of petiole rather thick at base, anterior surface slightly convex, posterior surface slightly concave, upper surface narrow and forming a rather sharp, ridge; gaster oval, not very voluminous, pointed at apex. Legs fairly long; tibiae prismatic. Long. 18 mm.
[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only the extreme anterior angle of clypens and cheeks blackish; the mandibles are pale yellow with the teeth red. The sculpture and hairs are similar.
Head long, narrow, broader in front than behind, broadest a little in front of sides of head, narrowed, rather sharply behind eyes to base; teeth to mandibles somewhat more slender and sharper, carinae on clypeus a little more pronounced; eyes more prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale of petiole of similar shape, but a little narrower; gaster and-legs of similar shape. Long. 10 - 12 mm.
Dodous bispinosus
Species
Public domain.
Very like
trispinosus
but without the two shorter spines on the mesonotum. The sculpture is different, and the species is also a little darker in colour.
[[ worker ]]. Head: the sculpture is quite different; the disc is smooth and shining, from the outer part of the smooth surface at sides semicircular carinae run on each side along the cheeks, and from the posterior part a few weaker carinae extend towards base of head, the space between these and the posterior border of head being smooth and shining.
Thorax: the ridges on the pronotum are considerably less marked; the mesonotum is smooth and shining and there are no spines present. The ridges on the sides of the thorax are less marked; the dorsal surface and the declivity of the epinotum are smooth and shining.
The spines on the pronotum are slightly longer and stronger, and those of the epinotum, being of a different shape, being slightly shorter, and projecting outwards then inwards in an even curve. Long. 5 mm.
Dodous trispinosus
Technomyrmex primroseae
Species
Public domain.
[[ worker ]]. Black, rather shining, mandibles, antennae and legs dirty pale yellow, the petiole brighter yellow. Sculpture: head and gaster finely reticulate, thorax more distinctly so, clothed with fine golden pubescence, which is more pronounced on gaster and a few short outstanding hairs, more being present on gaster.
Head oval, somewhat narrower in front than behind, broadest a little behind eyes, posterior angles rounded,. posterior border excised in middle; mandibles moderately long, triangular apical tooth sharp and curved, masticatory border armed with a number of small sharp teeth, the second and fourth being longer than the third; clypeus fairly large, anterior border excised in middle, posterior border extending in a point between the frontal carinae; frontal area small but distinct; frontal carinae short, low, fairly wide apart, parallel; eyes large, round, rather prominent, situated in front of sides of head; antennal 12 - jointed, scape long, extending beyond posterior border of head, funiculus with first joint longer than third, second joint the shortest, rest of joints gradually increasing in length and breadth, last joint as long as the two preceding taken together. Thorax with a neck, longer than broad, constricted in middle, broadest at humeral angles; pronotum large, transverse, convex, anterior border margined, posterior border semicircular encircling mesonotum; mesonotum shorter and narrower than pronotum, a little longer than broad, slightly convex; sutures between pro- and mesonotum and meso- and epinotum well marked, especially the latter; epinotum with angle between dorsal surface and declivity well marked, declivity abrupt, somewhat flat, considerably longer than dorsal surface. Petiole narrow, flat, slightly longer than broad, scale entirely rudimentary; gaster oval, overhanging the petiole, pointed at apex, fifth segment extending a little beyond the fourth, cloacial opening terminal. Long. 2.5 mm.
Edit above this line please
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http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq
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[[http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=narrow][http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=broad&associations=no]]
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[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=broad&associations=no&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][Click for RDF validation, triples and graph from the W3C online RDF validator]]
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* &associations=yes for each taxon name appearing in the treatment of the described taxon an spm:associatedTaxon is created inside an spmi:Associations
* &associations=no information about associated taxa is not returned
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[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx.xml&render=xhtml&description=narrow&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][Click for RDF validation, triples and graph from the W3C online RDF validator]]
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[[http://plazi.org Plazi]] is a non-profit organization dedicated to advancing open scientific literature. Its main project at the moment is the development of tools for automation of extraction of information from publications, whether scanned or born digital, and web services for applying and providing such information. This page is discusses an effort underway to use SPM to serve species descriptions, and related data from systematics literature. The work is funded by the Encyclopedia of Life and administered by GBIF and carried out for [[http://plazi.org Plazi]] by Main.TerryCatapano and Main.BobMorris.
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---++ Generally Current Example
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This is a complete rewrite and synthesis reflecting our understanding as of Oct 10 2008 and onward. It addresses remarks, answers, and questions made in earlier versions by Main.RogerHyam and Main.PatrickLeary and ourselves, including some simple things we were doing wrong. Thanks to Roger and Patrick for their comments.
a10 99
---+ SPM issues
---++Why SPM at all?
Patrick asked: Since a !TaxonConcept supports hasInformation, why wrap anything in a !SpeciesProfileModel?
We don't have an answer to this. Indeed it seems as though
....
blah, blah, blah
have exactly the same information content and semantics as
....
blah, blah, blah
---++Where to put citation?
!TaxonConcept has a property accordingTo, with value Actor. Actor has !CommonProperties. !CommonProperties has a data property !PublishedIn and object property !PublishedInCitation which has range !PublicationCitation. That is where we put it. This seems cumbersome to us, but for our application, in a given document, every described !TaxonConcept arises from extraction from a single journal publication, so we only need one such Actor and !PublicationCitation. We refer to it in each !TaxonConcept.accordingTo if there is more than one.
Is there something better to do?
---++Where to put LSID?
Answer, as Main.RogerHyam patiently pointed out: In an rdf:about on any object that needs one, especially !TaxonConcept and perhaps !PublishedInCitation when people start issuing LSIDs for journal articles. This seems to have two minor costs, mentioned next.
---++External references
A realistic use case for plazi involves external documents whose creators wish to make assertions that stuff in an SPM document is wrong. That is because plazi is extracting data from published literature, often originating in printed media, which may go through several processes subject to error. These include, imaging, OCR, semi-automated markup, and various transformations of the marked up data. Any of these might introduce errors that client applications may be able to detect and signal. Local IDs, especially with care about the xml:base, explicitly reify the RDF/XML object that they ID in a way that makes it easy to refer to them externally. But it doesn't look like absolute URIs such as required by rdf:about do so, so we don't presently know how to address support for external documents commenting upon the data in objects which have been given an rdf:about. A small example will be forthcoming here.
---++Other GUIDS
Journal publications, and perhaps other resources (e.g. people), may have other GUID schemes besides LSID in use to identify them Thus a resource may have several GUIDS (even several LSIDs). It therefore might be convenient if several GUIDs could be attached to a single object, e.g. the same !PublishedInCitation or the same !TaxonConcept.
As of 10 October 2008, we haven't thought of a good way to handle this.
---++More use of controlled vocabulary
One thing that I would like to see included is the use of tn:rank in addition to tn:rankString. It is always good as a consumer to get content in the form of a controlled vocabulary rather than trying to reconcile varying rankStrings which mean the same thing. -- Main.PatrickLeary - 30 Sep 2008
%GREEN%
In email to Terry I raised that point as follows:
I wonder how much effort it would be in the XSLT to embed the rank
terms from http://rs.tdwg.org/ontology/voc/TaxonRank#TaxonRankTerm
into the XSLT style sheet and if the tn:rankString you construct
matches one of the controlled strings, then also construct a tn:rank
object as well as a tn:rankString. I'm not entirely sure what is
gained from this, except that machine processing becomes more robust
and less dependent on string parsing. Issues that would arise in that
case include:
* What should a happen if there is no match?
* What breaks if the controlled tn:rank vocabulary changes?
-- Main.BobMorris - 01 Oct 2008 %ENDCOLOR%
---++ Where to put IPR and how to represent it?
%BLUE%
In RDF everything that is not a literal is a resource that is identified by a local id (possibly implied by the serialization) or a URI. It is therefore possible to assert licensing about any resource in an RDF graph simply by adding a dc:license or dc:rights property to it. The problem is with thinking in terms of XML serializations where it doesn't appear there is space for adding extra attributes.
-- RogerHyam - 6 Oct 2008 %ENDCOLOR%
My concern is whether this remains valid OWL-DL -- Main.BobMorris - 10 Oct 2008
Exactly how to represent it is really about the TDWG ontology in general, not something special to SPM or even citations. There was extensive discussion of what is and isn't copyrighted, what licenses apply, etc. That can be seen in an earlier version of this page and/or in such page as someone cares to link here. -- Main.BobMorris - 10 Oct 2008
---++ Line breaks and other document formatting
Patrick notes that there are no line breaks in the Descriptions plazi extracts and asks:
Is there some way to include line breaks - either using embedded escaped html or ensuring that newlines represent line breaks? -- Main.PatrickLeary - 30 Sep 2008
%GREEN% I am somewhere between nervous about, and opposed to, putting spurious (or any) html inside rdf. Most formatting chas no semantic content. In an extracted taxonomic description, formatting artefacts, especially from scanned documents, are just about the original rendition layout. A description might even have a page break in it, and in principle could even be interrupted by a figure (though I doubt any journal publisher would actually do that). Also, I think we don't even preserve any line breaks in !TaxonX, whence we are grabbing descriptions whose boundaries are determined by a !GoldenGate plugin. (Am I right Terry?). I guess that if there is escaped HTML in the text, then it remains as a string literal, but then it is going to be the client's responsibility to scan, parse, and interpret it. I don't have a full comprehension of http://www.w3.org/TR/rdf-concepts/#section-XMLLiteral but I think it may apply if you want some more robust XHTML in the text, rather than an uninterpreted escape sequence.
There _are_ some structural divisions identified by !GoldenGate within a description, but pending more sophisticated automatic markup than anybody does to date, it is not yet possible to put any semantics automatically on those divisions, and using them seems ugly and confusing. See the Sep 23 example, which we abandoned. -- Main.BobMorris - 01 Oct 2008 %ENDCOLOR%
GoldenGate currently marks up subsections within the treatment such as nomenclature (required for the taxonx output), ref-groups that include earlier citations of the taxon and as well nomenclatorial changes such as "new syn", Stat.nov." which relate the refs to the name of the treatment), description, discussion, materials_examined (the observation records listed), distribution (a summary of distribution records and its interpretation). Some of the elements are not always clear and can include several elements. But we do this mark-up routinely, and the GoldenGate editor is getting pretty efficient to figure out what section belongs to what item above.-- Main.DonatAgosti - 02 Oct 2008
---++ Namespace termination
It is pretty important to terminate namespace values with either '/' or '#'. Although failing to do so is valid RDF/XML serialization, it can result in ambiguity in the triple form of the RDF, wherein local name is concatenated with namespace to form resource names. Here's a good NamespaceTermination example from Adobe's XMP manual.
---+ Examples
---++ ObsoletePlaziExamples
a12 1
_[pending]_
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As of 30 Nov 2008, we offer a REST service requiring the user to choose one of two serializations, described below. The full api for the REST service follows those descriptions. In all cases, the document is returned as RDF/XML conforming to the definition of SPM. The API described below controls the content and rendering format of the spm:hasContent elements, which is what most clients will be inserting into their applications.
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@
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%META:TOPICINFO{author="BobMorris" date="1232084916" format="1.1" reprev="1.48" version="1.48"}%
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xx
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%META:TOPICINFO{author="TerryCatapano" date="1228106245" format="1.1" reprev="1.47" version="1.47"}%
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---++ Example of November 30
d143 1
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d150 11
a160 13
Donisthorpe, H. S. J. K.
A
new Camponotus from Madagascar and a small collection of ants from Mauritius.
Annals and
Magazine of Natural History
(12)2
1949
271-275
d164 2
a165 3
Not copyrightable.
d167 2
a168 3
d171 1
a171 2
d173 1
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a185 2
d187 5
a191 24
[[ soldier ]]. Very pale
dirty yellow, head reddish yellow, mandibles dark red, teeth, scapes,
anterior border of clypeus, and extreme anterior angles of cheeks black,
clothed with very sparse outstanding longer and shorter yellow hairs and
some fine very short decumbent yellow hairs. Sculpture consisting of very
fine reticulations, a little stronger on head.
Head large, triangular,
considerably broader behind than in front, broadest a little before
posterior angles, which are rounded and prominent, posterior border excised,
slightly sinuate on each side; mandibles massive, strongly punctured and
with transverse ridges, masticatory border armed with six large strong
teeth, the apical one being the longest, curved and sharp, the next two
longer and sharper than the last three;...
[[ worker ]] Of the same
pale colour as the [[ soldier ]]. but only the extreme anterior angle of
clypens and cheeks blackish; the mandibles are pale yellow with the teeth
red. The sculpture and hairs are similar.
Head long, narrow, broader
in front than behind, broadest a little in front of sides of head, narrowed,
rather sharply behind eyes to base; teeth to mandibles somewhat more slender
and sharper, carinae on clypeus a little more pronounced; eyes more
prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale
of petiole of similar shape, but a little narrower; gaster and-legs of
similar shape. Long. 10 - 12 mm.
d195 3
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a200 3
Not copyrightable.
d202 2
a203 3
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a206 2
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a220 2
d222 9
a230 18
Very like trispinosus but
without the two shorter spines on the mesonotum. The sculpture is different,
and the species is also a little darker in colour.
[[ worker ]]. Head: the
sculpture is quite different; the disc is smooth and shining, from the outer
part of the smooth surface at sides semicircular carinae run on each side
along the cheeks, and from the posterior part a few weaker carinae extend
towards base of head, the space between these and the posterior border of
head being smooth and shining.
Thorax: the ridges on the
pronotum are considerably less marked; the mesonotum is smooth and shining
and there are no spines present. The ridges on the sides of the thorax are
less marked; the dorsal surface and the declivity of the epinotum are smooth
and shining.
The spines on the pronotum
are slightly longer and stronger, and those of the epinotum, being of a
different shape, being slightly shorter, and projecting outwards then
inwards in an even curve. Long. 5 mm.
d234 28
a261 10
Dodous trispinosus
d263 23
a285 14
Dodous
...
@
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%META:TOPICINFO{author="BobMorris" date="1228101204" format="1.1" reprev="1.46" version="1.46"}%
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ObsoletePlaziExamples
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---++Recent Examples
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---++ Example of October 10
[[http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl][Click for the *current* result (i.e., not necessarily the same as the example below) of Plazi's REST service]] applied to the TaxonX version of Plazi document 5959. This may be slightly different from the example, which was fetched on October 10.
[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][Click for RDF validation, triples and graph of the *current* version (i.e., not necessarily the same as the example below) at the W3C online RDF validator]]
Donisthorpe, H. S. J. K.
A new Camponotus from Madagascar and a small collection of ants from Mauritius.
Annals and Magazine of Natural History
(12)2
1949
271-275
Camponotus (Tanaemyrmex) gerberti
Species
[[ soldier ]]. Very pale dirty yellow, head reddish yellow, mandibles dark red, teeth,
scapes, anterior border of clypeus, and extreme anterior angles of cheeks black, clothed with very
sparse outstanding longer and shorter yellow hairs and some fine very short decumbent yellow hairs.
Sculpture consisting of very fine reticulations, a little stronger on head.Head large, triangular,
considerably broader behind than in front, broadest a little before posterior angles, which are
rounded and prominent, posterior border excised, slightly sinuate on each side; mandibles massive,
strongly punctured and with transverse ridges, masticatory border armed with six large strong teeth,
the apical one being the longest, curved and sharp, the next two longer and sharper than the last
three; clypeus large, somewhat flat, carinate and slightly convex on disc, anterior border
considerably produced in middle where it is somewhat crenulate, and five large punctures are present
along the edge, and smaller punctures, rather wide apart, are scattered over the rest of the
surface, posterior border excised in middle; frontal area very faintly defined; frontal carinas
rather long, raised, with sharp edges, the rims or edges enclosing the antennal sockets are
considerably raised and prominent; a very fine narrow longitudinal ridge takes the place of the
frontal furrow and extends between the frontal carinae as far back as their extreme edges; eyes
large, broad oval, rather flat, are situated rather high up before the middle of the sides of the
head; antenna 12 - jointcd, scape long, thickened at apex, extending beyond the posterior border of
head funiculus with all the joints elongate, first slightly shorter than the others, last joint long
and pointed. Thorax longer than broad, broadest behind centre of sides of pronotum, somewhat slender
behind; pronotum ample. convex, with a short neck, sides margined, considerably widened afterneck,
posterior border semicircular; sutures between pro- and mesonotum, and meso- and epinotum fine but
distinct; mesonotum longer than broad, shorter than pronotum, somewhat flat on disc, sides rather
straight, epinotum longer than mesonotum, sides rather straight, angle between dorsal surface and
declivity not marked, dorsal surface longer than declivity. Scale of petiole rather thick at base,
anterior surface slightly convex, posterior surface slightly concave, upper surface narrow and
forming a rather sharp, ridge; gaster oval, not very voluminous, pointed at apex. Legs fairly long;
tibiae prismatic. Long. 18 mm.[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only
the extreme anterior angle of clypens and cheeks blackish; the mandibles are pale yellow with the
teeth red. The sculpture and hairs are similar.Head long, narrow, broader in front than behind,
broadest a little in front of sides of head, narrowed, rather sharply behind eyes to base; teeth to
mandibles somewhat more slender and sharper, carinae on clypeus a little more pronounced; eyes more
prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale of petiole of similar
shape, but a little narrower; gaster and-legs of similar shape. Long. 10 - 12 mm.
Dodous bispinosus
Species
Very like trispinosus but without the two shorter spines on the mesonotum. The
sculpture is different, and the species is also a little darker in colour. [[ worker ]]. Head: the
sculpture is quite different; the disc is smooth and shining, from the outer part of the smooth
surface at sides semicircular carinae run on each side along the cheeks, and from the posterior part
a few weaker carinae extend towards base of head, the space between these and the posterior border
of head being smooth and shining.Thorax: the ridges on the pronotum are considerably less marked;
the mesonotum is smooth and shining and there are no spines present. The ridges on the sides of the
thorax are less marked; the dorsal surface and the declivity of the epinotum are smooth and
shining.The spines on the pronotum are slightly longer and stronger, and those of the epinotum,
being of a different shape, being slightly shorter, and projecting outwards then inwards in an even
curve. Long. 5 mm.
-- Main.TerryCatapano - 10 Oct 2008
Edit above this line please
Ignore this please ... Bob Morris
As of 30 Nov 2008, we offer a REST service requiring the user to choose one of two serializations, described below. The full api for the REST service follows those descriptions. In all cases, the document is returned as RDF/XML conforming to the definition of SPM. The API described below controls the content and rendering format of the spm:hasContent elements, which is what most clients will be inserting into their applications.
d120 1
a120 3
1 &doc=[document name] This parameter sets the document to be retrieved as SPM
Use one of each pair of following parameters:
d122 1
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&description:
d124 13
a136 9
1 &description=narrow This parameter imposes a narrow view of what consitutes an spmi:Description. It extracts from a publication only the classical description, i.e. the characters and states that describe the taxon under consideration, for insertion into the appropriate spm:hasContent element.
1 &description=broad This parameter imposes a broad view of an spmi:Description. Application of it in the REST service results in all of the sections of a treatment returned, e.g. _materials examined_, _description_, _diagnosis_, _etymology_, etc., separated from one another in ways that identify them. These appear in the appropriate spm:hasContent element. For future work we will propose a controlled vocabulary for these parts of a treatment so that they can be marked up more explicitly in RDF.
&render:
1 &render=text The spm:hasContent items are plain text, with paragraphs separated by white space.
1 &render=xhtml The spm:hasContent items are xhtml with character entities require escaping. This rendering will require that a client filters the escaped entities, particularly the xhtml escaped brackets, to turn it into xhtml suitable for browsers.
--++ Example of November 30
a142 1
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a145 1
Not copyrightable.
d156 1
a156 1
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a197 1
longer and sharper than the last three; ...
d215 1
d278 1
a278 4
...
d281 1
@
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%META:TOPICINFO{author="BobMorris" date="1228094832" format="1.1" version="1.45"}%
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[[http://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx1.xml&render=xhtml&description=narrow][doc=5959_tx1.xmlhttp://plazi.cs.umb.edu:8080/exist/rest/db/taxonx_docs/getSPM.xq?doc=5959_tx1.xml&render=text&description=narrow&render=xhtml&description=narrow]]
@
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@d1 1
a1 1
%META:TOPICINFO{author="TerryCatapano" date="1228087142" format="1.1" version="1.44"}%
d234 1
a234 1
As of 30 Nov 2008, we offer a REST service requiring the user to choose one of two serializations, described below. The full api for the REST service follows those descriptions.
d244 2
a245 2
1 &description=narrow This parameter imposes a narrow view of what consitutes an spmi:Description. It extracts from a publication only the classical description, i.e. the characters and states that describe the taxon under consideration.
1 &description=broad This parameter imposes a broad view of an spmi:Description. Application of it in the REST service results in all of the sections of a treatment returned, e.g. _materials examined_, _description_, _diagnosis_, _etymology_, etc., separated from one another in ways that identify them. For future work we will propose a controlled vocabulary for these parts of a treatment
d249 2
a250 2
1 &render=text This is plain text, with paragraphs separated by white space.
1 &render=xhtml This is xhtml with character entities require escaping. This rendering will require that a client filters the escaped entities, particularly the xhtml escaped brackets, to turn it into xhtml suitable for browsers.
@
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%META:TOPICINFO{author="TerryCatapano" date="1228072840" format="1.1" reprev="1.43" version="1.43"}%
@
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%META:TOPICINFO{author="BobMorris" date="1227302918" format="1.1" version="1.42"}%
d234 1
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As of 21 Nov 2008, we offer a REST service requiring the user to choose one of two XSL style sheets, described below. The full api for the REST service follows those descriptions.
d236 1
a236 2
1 SS1.xsl This style sheet imposes a narrow view of what consitutes an spmi:Description. It extracts from a publication only the classical description, i.e. the characters and states that describe the taxon under consideration.
1 SS1.xsl This style sheet imposes a broad view of an spmi:Description. Application of it in the REST service results in all of the sections of a treatment returned, e.g. _materials examined_, _description_, _diagnosis_, _etymology_, etc., separated from one another in ways that identify them. For future work we will propose a controlled vocabulary for these parts of a treatment
d238 1
a238 3
In addition to the current choice of style sheets providing differnt views as above, we also support two rendering choices given by a key named _render_ with values one of:
1 _text_ This is plain text, with paragraphs separated by white space.
1 _xhtml_ This is xhtml with character entities require escaping. This rendering will require that a client filters the escaped entities, particularly the xhtml escaped brackets, to turn it into xhtml suitable for browsers.
d240 1
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@
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%META:TOPICINFO{author="TerryCatapano" date="1225909621" format="1.1" version="1.41"}%
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@
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%META:TOPICINFO{author="TerryCatapano" date="1224671552" format="1.1" version="1.40"}%
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[[http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl][Click for the *current* result (i.e., not necessarily the same as the example below) of Plazi's REST service]] applied to the TaxonX version of Plazi document 5959. This may be slightly different from the example, which was fetched on October 10.
d122 1
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[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][Click for RDF validation, triples and graph of the *current* version (i.e., not necessarily the same as the example below) at the W3C online RDF validator]]
@
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%META:TOPICINFO{author="PatrickLeary" date="1224508524" format="1.1" version="1.39"}%
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[[http://plazi.org Plazi]] is a non-profit organization dedicated to advancing open scientific literature. Its main project at the moment is the development of tools for automation of extraction of information from publications, whether scanned or born digital, and web services for applying and providing such information. This page is discusses an effort underway to use SPM to serve species descriptions, and related data from systematics literature. The work is funded by the Encyclopedia of Life and administered by GBIF and carried out by Main.TerryCatapano and Main.BobMorris.
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%TOC%
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This is a complete rewrite and synthesis reflecting our understanding as of Oct 10 2008 and onward. It addresses remarks, answers, and questions made in earlier versions by Main.RogerHyam and Main.PatrickLeary, including some simple things we were doing wrong. Thanks to both for their comments.
d44 1
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!TaxonConcept has a property accordingTo, with value Actor. Actor has !CommonProperties; !CommonProperties has a data property !PublishedIn and object property !PublishedInCitation which has range !PublicationCitation. This seems cumbersome to us, but in our application, in a given document, every described !TaxonConcept is arises from extraction from a single journal publication. We cite that once (i.e. we have a single Actor and !PublicationCitation), refer to it in each !TaxonConcept.accordingTo if there is more than one !TaxonConcept in the document, as is usually the case.
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%GREEN% I am somewhere between nervous about, and opposed to, putting spurious (or any) html inside rdf. Many formatting artefacts certainly have no semantic content. In an extracted description are just about the paper rendition layout. A description might even have a page break in it, and in principle could even be interrupted by a figure (though I doubt any journal publisher would actually do that). Also, I think we don't even preserve any line breaks in !TaxonX, whence we are grabbing descriptions whose boundaries are determined by a !GoldenGate plugin. (Am I right Terry?). I guess that if there is escaped HTML in the text, then it remains as a string literal, but then it is going to be the client's responsibility to scan, parse, and interpret it. I don't have a full comprehension of http://www.w3.org/TR/rdf-concepts/#section-XMLLiteral but I think it may apply if you want some more robust XHTML in the text, rather than an uninterpreted escape sequence.
@
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%META:TOPICINFO{author="TerryCatapano" date="1223668889" format="1.1" reprev="1.33" version="1.33"}%
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---++ TDWG ontology defects obstructing SPM deployment
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---+++ !TaxonConcept
---++++No place to put publication
The !TaxonConcept RDF at http://rs.tdwg.org/ontology/voc/TaxonConcept does not appear to support any property for the publication in which the accordingTo, e.g. in an SPM aboutTaxon, may have appeared. Discussion should cross reference the TDWG [[http://rs.tdwg.org/ontology/voc/TaxonConcept !TaxonConcept DiscussionPage]]. - 25 Aug 2008
a7 1
Bob and Terry reply: accordingTo is an Actor; Actor has !CommonProperties; !CommonProperties has a data property !PublishedIn and object property !PublishedInCitation which has range !PublicationCitation Is that where we should put the publication? Probably yes say Terry and Bob on Oct 1, 2008. However, separately, we still can't find a place to put the lsid for either the !TaxonConcept or for the publication. below. -- Main.BobMorris, Main.TerryCatapano - 01 Oct 2008
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Note that the Initial Example of 25 Aug 2008 below has an aboutTaxon !TaxonConcept which is locally defined and which would give no hint as to the publication in which the !TaxonConcept is defined. Since this is most of the point of the plazi effort, that is a serious deficiency. -- Main.BobMorris - 25 Aug 2008
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---++++No place to put lsids
In a number of circumstances (e.g. !TaxonConcept, and !PublicationCitation) we find no place to put an lsid that corresponds to the object. One possibility is to extend SPM so that it has an !InfoItem class named something like GUID, which has an object property guidValue and one named guidType that includes some named types including lsid, doi, isbn, issn, handles, ITIS ids, .... Some of these are already types appearing in !PublicationCitation and care may be needed to guarantee consistency if a new usage of those is adopted. As of Oct 1, we hang it on, e.g. !TaxonConcept.hasInformation@@rdfResource. This makes it the object of the triple <taxonConcept, hasInformation, rdfResource>-- Main.BobMorris, Main.TerryCatapano - 01 Oct 2008
---++ Examples
ObsoletePlaziExamples
---+++ Recent Examples
Some issues arrising from Example of Sep 6 found on ObsoletePlaziExamples:
Result of validation at w3c Validation Service at http://www.w3.org/RDF/Validator/:
Error: {W108} Not an XML Name: 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722'[Line = 2, Column = 87]
Error: {W108} Not an XML Name: 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722_Description_1'[Line = 4, Column = 94]
Error: {W105} Redefinition of ID: urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722[Line = 9, Column = 79]
Error: {W105} Previous definition of 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722'.[Line = 2, Column = 87]
Error: {W108} Not an XML Name: 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722'[Line = 9, Column = 79]
Error: {W105} Redefinition of ID: urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722[Line = 14, Column = 80]
Error: {W105} Previous definition of 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722'.[Line = 2, Column = 87]
Error: {W108} Not an XML Name: 'urn:lsid:biosci.ohio-state.edu:osuc_concepts:186722'[Line = 14, Column = 80]
Two problems here. Using LSID's for rdf:ID causes error because it is not of the XML Name datatype. That's not a big deal as we can change the strings to make them valid. The bigger problem is the second problem. Are we really to make *all* assertions about the same rdf:ID under the same element? Is rdf:ID like xsd:id and id'ing an element, not a concept? Should we be using something like rdf:about for this purpose?
---
I believe rdf:ID is simply a node id unique in the rdf graph, which for RDF/XML would seem to translate to your first conclusion: it is an id on the element. I'm not sure what would be meant by an _RDF concept_. In the pantheon of languages expressed in RDF, RDF has properties, but no Classes. Those are defined in RDFS, the next layer up. I guess most people would say that an rdfs:Class defines a concept (whose circumscription is all the things which have that class as their datatype.). Given this, I would say that there is no other conclusion but that rdf:id is id'ing an element.
I think rdf:about is not any better for what you may be trying to do. rdf:about is used most often as an attribute of rdf:Description. As above, you can't describe classes purely in RDF, so either we have to escalate to rdfs, which is probably not profitable, or we try to solve the problem entirely in the TDWG lsid vocabularies, which are all in the OWL layer (and in particular, have plenty of classes defined).
Is the issue really how do we make assertions about the Taxon Concept behind the lsid? (as opposed to the lsid, which itself is just an rdf literal, and not much worth describing. In fact lsid's are supposed to be semantically opaque). To get the TC behind an lsid requires resolution. This makes me worry that if we know an lsid, we may have to do the resolution on the way to constructing the SPM....that sounds nasty, and also needs a failover strategy in case the lsid does not resolve, its contract notwithstanding. It also seems to require that the lsid resolution actually presents a TDWG !TaxonConcept object expressed in (or convertible to) lsid voc.
It may be that the only way out is that the lsid's we can discover or generate are simply the content (or value) of another InfoItem. In turn, that might require a new class of InfoItem named, e.g. LSID.
-- Main.BobMorris - 07 Sep 2008
---+++ New Proposal: 17 Sep 2008
On ObsoletePlaziExamples in his proposal of 17 Sep 2008, Main.TerryCatapano comments:
based on reading of RDF Syntax Spec http://www.w3.org/TR/rdf-syntax-grammar
rdf:id's function is to reify triples and extends base url given in xml:base (which is the uri of the rdf doc?)
using rdf:about to specify that taxon concept LSID is the subject of the SPM
use rdf:resource to specify that the concept LSID is the concept of the about LSID -- not sure about this as it is recursive (A has concept A)?
This at least validates, however.
Main.ChuckMiller asks:
Why can't you use the accordingToString property for TaxonConcept to solve this problem? Like this
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Monomorium clarinodis Heterick
Species
Journal of Whatever, Vol. X, p. Y
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-- Main.ChuckMiller - 18 Sep 2008
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Main.BobMorris replies:
There's nothing wrong with this (well, nothing that isn't also a problem with the part of Terry's 17 Sep proposal. See below). However, it doesn't address the original, somewhat technical, problem Terry raised on Sep 6. That problem was essentially "How is it assured that the different elements of a !SpeciesProfileModel object all refer to the same taxon concept in the face of the fact that rdf:ID values must be unique in the document?" Terry's s proposed solution on Sep 17 is that rdf:ID not the right mechanism to solve the problem, since it is meant to identify an element in the document, not to identify stuff that the element is talking about. Instead, the appropriate thing to do is add an rdf:resource attribute and hang the LSID there. I think the main reason this is an issue at all is that an SPM can discuss other taxon concepts besides the one it is about. This use of rdf:resource seems to be the approach of most of the TDWG-based examples on the TDWG lsid resolver proxy service described at http://lsid.tdwg.org/.
I see these problems remaining:
* It's unclear to me that the current TDWG ontology definitions even allow for attributes to be hung on a the tc:TaxonConcept in the first place (or on any other defined rdf element for that matter...). I wonder if this means that while the proposed SPM is valid RDF, it may not be valid OWL. %BLUE% As a TaxonConcept is a resource then it has a URI or local node id and so any assertion can be made about it (it can be the subject of a triplet). I don't understand why you don't understand otherwise I would say it another way to try and help -- RogerHyam - 6 Oct 2008 %BLACK%
* What semantics is imposed on rdf:resource whose value is the lsid of a tc:TaxonConcept that would insure that relevant string data in the resolved !TaxonConcept is in any way related (preferably is the same as) the string data offered in the document. Unless the document string data were generated by _resolving_ the lsid (and maybe even then if the TC object is returned in the lsid metadata and not its data) there can be no such guarantee. Indeed, the Hymenoptera Name Server lsids return everything in the metadata. The lsid might resolve to something that is not even meaningfully the same as the one described by the string data. I raised that problem when the original Sep 6 issue was raised. %BLUE% Are you talking about receiving data from different sources that describe the same thing? If so then it is up to the client to track where it receives assertions from and whether it trusts those sources. This would be done using named graphs typically. It is exactly the same problem as merging any two documents. -- RogerHyam - 6 October 2008 %BLACK%
-- Main.BobMorris - 19 Sep 2008
OK, Terry and I are in agreement (and a little chagrined at getting it wrong) that Roger is completely right that it is appropriate to use rdf:about on objects and that this presents no issues within the generated document. We do this now. It does leave us with a separate, smaller, issue that puzzles us and which is a little relevant to what plazi's SPM is supposed to do. Hopefully this is as easy and we simply still overlook something simple. This is about reification and reference in external documents whose creators wish to make assertions that stuff in an SPM document is wrong. This is a realistic use-case because plazi is extracting data from published literature, often originating in printed media, which may go through several processes, (e.g. imaging, OCR, semi-automated markup, and various transformations of the marked up data) any of which might introduce errors that client applications might be able to detect and signal. Local IDs, especially with care about the xml:base, explicitly reify the RDF/XML object they ID in a way that makes it easy to refer to them externally. But it doesn't look like absolute URIs such as required by rdf:about do so, so we don't presently know how to address this. A small example will be forthcoming here. -- Main.BobMorris - 08 Oct 2008
---++ Namespace termination
It is pretty important to terminate namespace values with either '/' or '#'. Although failing to do so is valid RDF/XML serialization, it can result in ambiguity in the triple form of the RDF, wherein local name is concatenated with namespace to form resource names. Here's a good NamespaceTermination example from Adobe's XMP manual.
[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][For validation, triples and graph of the *current* version (i.e., not necessarily the same as the example below) at W3C online validator]]
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---++ Clarification Needed
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I have looked through this latest example and yesterday talked with Bob Morris about some outstanding issues (or uncertainty on my part) with this last version (24 September - see attached). One issue that remains vital to EOL is that of intellectual property and licensing. I raised the issue that there is no statement of licensing of the content being shared. Bob was of the idea that biological descriptions are statements of fact and are not intellectual property, therefore they cannot be licensed. I am not an IP lawyer so have asked that EOL look into this. I would be interested to see how licensing would appear if the description shared were in fact intellectual property. EOL will need to make recommendations on what standards to use and how to use them, and some content partners will want to share text that is copyrighted.
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I raised the question of how do we cite the descriptions. I see that each spm:SpeciesProfileModel has a spm:aboutTaxon which should ultimately reference a PublicationCitation with publishedIn. I can see that we can clearly cite the source of the taxon concept, but can we always infer that the publishedIn for the taxon is the same source of the description? What if I write a description on my own website, but cite person X's concept of the organism? Either way, it would be great to have a clear statement about the recommended way to infer the proper way to attribution statement for the description. This is also important for EOL and very important for those contributing content of their own. -- Main.PatrickLeary - 30 Sep 2008
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%GREEN% Possibly this discussion belongs in some other venue. It doesn't seem unique to SPM. To the extent that a data provider asserts that their data are not subject to copyright because not creative works, we need a machine-readable mechanism that signals this---perhaps with a reason,---so that an application can choose whether to republish the data. -- Main.BobMorris - 01 Oct 2008 %ENDCOLOR%
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Regarding Patrick's comment about Bob's comment "Bob was of the idea that biological descriptions are statements of fact and are not intellectual property, therefore they cannot be licensed." The SPM needs to be capable of capturing the attribution data associated with the content and this attribution data can vary a lot. We can't just jump to the conclusion that all content is a fact and therefore unattributed. In science, I might think there is nothing that should be unattributed. This is different than "copyrighted". Content can be attributed without being copyrighted. For instance, there are plenty of authors of public domain content who get attribution. Can we address this area as "attribution" versus "intellectual property"? Some content attributions are in fact for copyright, others are not. How can the fact of a "some rights reserved" license like Creative Commons be included with the object? SPM should be capable to include all of the needed data elements to capture the attribution facts of the content. For the EOL's dataObject in its Transfer Schema, this has led to the use of new "agent" elements with roles of Source, Author, Project, and Publisher, combined with the elements dc:Rights, dcterms:RightsHolder, dcterms:bibliographicCitation, and dc:source. Also dc:description is used for the actual text content. We need to be able to include attribution facts in the SPM along with the scientific facts.-- Main.ChuckMiller - 01 Oct 2008
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%BLUE%
In RDF everything that is not a literal is a resource that is identified by a local id (possibly implied by the serialization) or a URI. It is therefore possible to assert licensing about any resource in an RDF graph simply by adding a dc:license or dc:rights property to it. The problem is with thinking in terms of XML serializations where it doesn't appear there is space for adding extra attributes.
-- RogerHyam - 6 Oct 2008
%BLACK%
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Note for Plazi: there are no line breaks in the text in this document. It seems that newlines in the descriptions do not represent line breaks (see #_Description_2_1). Is there some way to include line breaks - either using embedded escaped html or ensuring that newlines represent line breaks? -- Main.PatrickLeary - 30 Sep 2008
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GoldenGate currently marks up subsections within the treatment such as nomenclature (required for the taxonx output), ref-groups that include earlier citations of the taxon and as well nomenclatorial changes such as "new syn", Stat.nov." which relate the refs to the name of the treatment), description, discussion, materials_examined (the observation records listed), distribution (a summary of distribution records and its interpretation). Some of the elements are not always clear and can include several elements. But we do this mark-up routinely, and the GoldenGate editor is getting pretty efficient to figure out what section belongs to what item above.
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-- Main.DonatAgosti - 02 Oct 2008
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---+++ More Questions
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I have been playing with this latest example a bit more today and have some new questions. The taxonConcepts use tc:hasInformation to point to the resource which describe the taxonConcept, but according to the standard tx:hasInformation should point to an infoItem, not a taxonConcept. So, is this invalid at this point? -- Main.PatrickLeary - 30 Sep 2008
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%GREEN%Yep, you are right. Will fix in next release. We have to set up an OWL validator to catch stuff like this..... We are just using it as a place to hang the LSID of the taxonConcept. Terry and I talked about where to hang the LSID and this seemed appropriate. Have to check whether it is still OWL valid.... In general, I want to raise in Fremantle whether there are or should be best practices about where to squirrel LSIDs.-- Main.BobMorris - 01 Oct 2008 %ENDCOLOR%
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I also have a bit of a naive question, but one I would like to understand. SpeciesProfileModel contains two main elements which are of class taxonConcept and infoItem. The SPM element I suppose binds these two elements. But, if taxonConcept contains a hasInformation element, which is also an infoItem - couldn't we just have one RDF document which contains a bunch of taxonConcepts which have zero to many infoItems? In this latest example there are several SPM elements which only contain an aboutTaxon and it seems a bit unnecessary to have this extra SPM wrapper. I would be just as happy having a bunch of taxonConcepts, some of which contain infoItems.-- Main.PatrickLeary - 30 Sep 2008
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%GREEN%We are presently scratching our heads to see if there are scenarios where your proposal doesn't work. So far don't have any... -- Main.BobMorris, Main.TerryCatapano - 01 Oct 2008 %ENDCOLOR%
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[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][For validation, triples and graph of the *current* version (i.e., not necessarily the same as the example below) at W3C online validator]]
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xmlns:spmi="http://rs.tdwg.org/ontology/voc/SPMInfoItems#" xmlns:tbase="http://rs.tdwg.org/ontology/Base#"
xmlns:tcom="http://rs.tdwg.org/ontology/voc/Common#"
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---+++ Example of October 1
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* created tbase:Actor to contain publication info referenced from tc:accordingTo in tc:TaxonConcept
* moved aboutTaxon to be 1st child of spm:SpeciesProfileModel
* filtered out treatments without description sections
* still not OWL valid because of use of rdf:resource on ?hasInformation for LSID
Donisthorpe, H. S. J. K.
A new Camponotus from Madagascar and a small collection of ants from Mauritius.
Annals and Magazine of Natural History
(12)2
1949
271-275
Camponotus (Tanaemyrmex) gerberti
Species
[[ soldier ]]. Very pale dirty yellow, head reddish yellow, mandibles dark red, teeth, scapes, anterior border of clypeus, and extreme anterior angles of cheeks black, clothed with very sparse outstanding longer and shorter yellow hairs and some fine very short decumbent yellow hairs. Sculpture consisting of very fine reticulations, a little stronger on head.Head large, triangular, considerably broader behind than in front, broadest a little before posterior angles, which are rounded and prominent, posterior border excised, slightly sinuate on each side; mandibles massive, strongly punctured and with transverse ridges, masticatory border armed with six large strong teeth, the apical one being the longest, curved and sharp, the next two longer and sharper than the last three; clypeus large, somewhat flat, carinate and slightly convex on disc, anterior border considerably produced in middle where it is somewhat crenulate, and five large punctures are present along the edge, and smaller punctures, rather wide apart, are scattered over the rest of the surface, posterior border excised in middle; frontal area very faintly defined; frontal carinas rather long, raised, with sharp edges, the rims or edges enclosing the antennal sockets are considerably raised and prominent; a very fine narrow longitudinal ridge takes the place of the frontal furrow and extends between the frontal carinae as far back as their extreme edges; eyes large, broad oval, rather flat, are situated rather high up before the middle of the sides of the head; antenna 12 - jointcd, scape long, thickened at apex, extending beyond the posterior border of head funiculus with all the joints elongate, first slightly shorter than the others, last joint long and pointed. Thorax longer than broad, broadest behind centre of sides of pronotum, somewhat slender behind; pronotum ample. convex, with a short neck, sides margined, considerably widened afterneck, posterior border semicircular; sutures between pro- and mesonotum, and meso- and epinotum fine but distinct; mesonotum longer than broad, shorter than pronotum, somewhat flat on disc, sides rather straight, epinotum longer than mesonotum, sides rather straight, angle between dorsal surface and declivity not marked, dorsal surface longer than declivity. Scale of petiole rather thick at base, anterior surface slightly convex, posterior surface slightly concave, upper surface narrow and forming a rather sharp, ridge; gaster oval, not very voluminous, pointed at apex. Legs fairly long; tibiae prismatic. Long. 18 mm.[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only the extreme anterior angle of clypens and cheeks blackish; the mandibles are pale yellow with the teeth red. The sculpture and hairs are similar.Head long, narrow, broader in front than behind, broadest a little in front of sides of head, narrowed, rather sharply behind eyes to base; teeth to mandibles somewhat more slender and sharper, carinae on clypeus a little more pronounced; eyes more prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale of petiole of similar shape, but a little narrower; gaster and-legs of similar shape. Long. 10 - 12 mm.
Dodous bispinosus
Species
Very like
trispinosus
but without the two shorter spines on the mesonotum. The sculpture is different, and the species is also a little darker in colour.
[[ worker ]]. Head: the sculpture is quite different; the disc is smooth and shining, from the outer part of the smooth surface at sides semicircular carinae run on each side along the cheeks, and from the posterior part a few weaker carinae extend towards base of head, the space between these and the posterior border of head being smooth and shining.Thorax: the ridges on the pronotum are considerably less marked; the mesonotum is smooth and shining and there are no spines present. The ridges on the sides of the thorax are less marked; the dorsal surface and the declivity of the epinotum are smooth and shining.The spines on the pronotum are slightly longer and stronger, and those of the epinotum, being of a different shape, being slightly shorter, and projecting outwards then inwards in an even curve. Long. 5 mm.
Technomyrmex primroseae
Species
[[ worker ]]. Black, rather shining, mandibles, antennae and legs dirty pale yellow, the petiole brighter yellow. Sculpture: head and gaster finely reticulate, thorax more distinctly so, clothed with fine golden pubescence, which is more pronounced on gaster and a few short outstanding hairs, more being present on gaster.Head oval, somewhat narrower in front than behind, broadest a little behind eyes, posterior angles rounded,. posterior border excised in middle; mandibles moderately long, triangular apical tooth sharp and curved, masticatory border armed with a number of small sharp teeth, the second and fourth being longer than the third; clypeus fairly large, anterior border excised in middle, posterior border extending in a point between the frontal carinae; frontal area small but distinct; frontal carinae short, low, fairly wide apart, parallel; eyes large, round, rather prominent, situated in front of sides of head; antennal 12 - jointed, scape long, extending beyond posterior border of head, funiculus with first joint longer than third, second joint the shortest, rest of joints gradually increasing in length and breadth, last joint as long as the two preceding taken together. Thorax with a neck, longer than broad, constricted in middle, broadest at humeral angles; pronotum large, transverse, convex, anterior border margined, posterior border semicircular encircling mesonotum; mesonotum shorter and narrower than pronotum, a little longer than broad, slightly convex; sutures between pro- and mesonotum and meso- and epinotum well marked, especially the latter; epinotum with angle between dorsal surface and declivity well marked, declivity abrupt, somewhat flat, considerably longer than dorsal surface. Petiole narrow, flat, slightly longer than broad, scale entirely rudimentary; gaster oval, overhanging the petiole, pointed at apex, fifth segment extending a little beyond the fourth, cloacial opening terminal. Long. 2.5 mm.
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---+++ Example of 24 September 2008
a103 148
* With proper handling of rank.
* hasContent now for each Description section, not each Paragraph in the Description
[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][For validation, triples and graph of the *current* version (i.e., not necessarily the same as the example below) at W3C online validator]]
[[ soldier ]]. Very pale dirty yellow, head reddish yellow, mandibles dark red, teeth,
scapes, anterior border of clypeus, and extreme anterior angles of cheeks black, clothed with very
sparse outstanding longer and shorter yellow hairs and some fine very short decumbent yellow hairs.
Sculpture consisting of very fine reticulations, a little stronger on head.Head large, triangular,
considerably broader behind than in front, broadest a little before posterior angles, which are
rounded and prominent, posterior border excised, slightly sinuate on each side; mandibles massive,
strongly punctured and with transverse ridges, masticatory border armed with six large strong teeth,
the apical one being the longest, curved and sharp, the next two longer and sharper than the last
three; clypeus large, somewhat flat, carinate and slightly convex on disc, anterior border
considerably produced in middle where it is somewhat crenulate, and five large punctures are present
along the edge, and smaller punctures, rather wide apart, are scattered over the rest of the
surface, posterior border excised in middle; frontal area very faintly defined; frontal carinas
rather long, raised, with sharp edges, the rims or edges enclosing the antennal sockets are
considerably raised and prominent; a very fine narrow longitudinal ridge takes the place of the
frontal furrow and extends between the frontal carinae as far back as their extreme edges; eyes
large, broad oval, rather flat, are situated rather high up before the middle of the sides of the
head; antenna 12 - jointcd, scape long, thickened at apex, extending beyond the posterior border of
head funiculus with all the joints elongate, first slightly shorter than the others, last joint long
and pointed. Thorax longer than broad, broadest behind centre of sides of pronotum, somewhat slender
behind; pronotum ample. convex, with a short neck, sides margined, considerably widened afterneck,
posterior border semicircular; sutures between pro- and mesonotum, and meso- and epinotum fine but
distinct; mesonotum longer than broad, shorter than pronotum, somewhat flat on disc, sides rather
straight, epinotum longer than mesonotum, sides rather straight, angle between dorsal surface and
declivity not marked, dorsal surface longer than declivity. Scale of petiole rather thick at base,
anterior surface slightly convex, posterior surface slightly concave, upper surface narrow and
forming a rather sharp, ridge; gaster oval, not very voluminous, pointed at apex. Legs fairly long;
tibiae prismatic. Long. 18 mm.[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only
the extreme anterior angle of clypens and cheeks blackish; the mandibles are pale yellow with the
teeth red. The sculpture and hairs are similar.Head long, narrow, broader in front than behind,
broadest a little in front of sides of head, narrowed, rather sharply behind eyes to base; teeth to
mandibles somewhat more slender and sharper, carinae on clypeus a little more pronounced; eyes more
prominent. Thorax narrow and slender; pronotum more narrowed to apex. Scale of petiole of similar
shape, but a little narrower; gaster and-legs of similar shape. Long. 10 - 12 mm.
Camponotus (Tanaemyrmex) gerberti
Species
Very like trispinosus but without the two shorter spines on the mesonotum. The
sculpture is different, and the species is also a little darker in colour. [[ worker ]]. Head: the
sculpture is quite different; the disc is smooth and shining, from the outer part of the smooth
surface at sides semicircular carinae run on each side along the cheeks, and from the posterior part
a few weaker carinae extend towards base of head, the space between these and the posterior border
of head being smooth and shining.Thorax: the ridges on the pronotum are considerably less marked;
the mesonotum is smooth and shining and there are no spines present. The ridges on the sides of the
thorax are less marked; the dorsal surface and the declivity of the epinotum are smooth and
shining.The spines on the pronotum are slightly longer and stronger, and those of the epinotum,
being of a different shape, being slightly shorter, and projecting outwards then inwards in an even
curve. Long. 5 mm.
Dodous bispinosus
Species
Solenopsis mameti Donisthorpe
Species
[[ worker ]]. Black, rather shining, mandibles, antennae and legs dirty pale yellow, the
petiole brighter yellow. Sculpture: head and gaster finely reticulate, thorax more distinctly so,
clothed with fine golden pubescence, which is more pronounced on gaster and a few short outstanding
hairs, more being present on gaster.Head oval, somewhat narrower in front than behind, broadest a
little behind eyes, posterior angles rounded,. posterior border excised in middle; mandibles
moderately long, triangular apical tooth sharp and curved, masticatory border armed with a number of
small sharp teeth, the second and fourth being longer than the third; clypeus fairly large, anterior
border excised in middle, posterior border extending in a point between the frontal carinae; frontal
area small but distinct; frontal carinae short, low, fairly wide apart, parallel; eyes large, round,
rather prominent, situated in front of sides of head; antennal 12 - jointed, scape long, extending
beyond posterior border of head, funiculus with first joint longer than third, second joint the
shortest, rest of joints gradually increasing in length and breadth, last joint as long as the two
preceding taken together. Thorax with a neck, longer than broad, constricted in middle, broadest at
humeral angles; pronotum large, transverse, convex, anterior border margined, posterior border
semicircular encircling mesonotum; mesonotum shorter and narrower than pronotum, a little longer
than broad, slightly convex; sutures between pro- and mesonotum and meso- and epinotum well marked,
especially the latter; epinotum with angle between dorsal surface and declivity well marked,
declivity abrupt, somewhat flat, considerably longer than dorsal surface. Petiole narrow, flat,
slightly longer than broad, scale entirely rudimentary; gaster oval, overhanging the petiole,
pointed at apex, fifth segment extending a little beyond the fourth, cloacial opening terminal.
Long. 2.5 mm.
Technomyrmex primroseae
Species
etc...
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* It's unclear to me that the current TDWG ontology definitions even allow for attributes to be hung on a the tc:TaxonConcept in the first place (or on any other defined rdf element for that matter...). I wonder if this means that while the proposed SPM is valid RDF, it may not be valid OWL.
* What semantics is imposed on rdf:resource whose value is the lsid of a tc:TaxonConcept that would insure that relevant string data in the resolved !TaxonConcept is in any way related (preferably is the same as) the string data offered in the document. Unless the document string data were generated by _resolving_ the lsid (and maybe even then if the TC object is returned in the lsid metadata and not its data) there can be no such guarantee. Indeed, the Hymenoptera Name Server lsids return everything in the metadata. The lsid might resolve to something that is not even meaningfully the same as the one described by the string data. I raised that problem when the original Sep 6 issue was raised.
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The !TaxonConcept RDF at http://rs.tdwg.org/ontology/voc/TaxonConcept does not appear to support any property for the publication in which the accordingTo, e.g. in an SPM aboutTaxon, may have appeared. Discussion should cross reference the TDWG [[http://rs.tdwg.org/ontology/voc/TaxonConcept !TaxonConcept DiscussionPage]]
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---++ Deprecation of tc:rankString
---+++ Example of 23 September 2008
Some changes:
* SPM doc itself is subject of spm:SpeciesProfileModel (via xml:base)
* no non-referenced namespace declarations
* an spmi:Description now for each *paragraph* under a tax:Description element
* spm:aboutTaxon now includes tc:hasInformation with LSID of concept as value of rdf:resource
* use "en" for "nomenclatural language"?
However, this example uses a deprecated treatment of rank.
[[http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept][see wiki page]]
*Deprecated* The taxonomic rank of this concept as a string. A string representation of the rank of this concept. It is highly recommended that the rank property be used along with this one unless the correct rank is not available in the rank vocabulary. No direct equivalent in TCS but is string version of /DataSet/TaxonConcepts/TaxonConcept/Rank. Requested by data suppliers. After discussions between a number of parties this property is considered to be deprecated. The rank of a TaxonConcept should be indicated by including a TaxonName of the appropriate rank in the hasName property even if the name object is empty apart from the rank.
---
[[http://www.w3.org/RDF/Validator/ARPServlet?URI=http://plazi.cs.umb.edu:8180/exist/rest/db/taxonx_docs/5959_tx1.xml?_xsl=styles/tx2spm.xsl&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_BOTH&FORMAT=PNG_EMBED][For validation, triples and graph at W3C online validator]]
[[ soldier ]]. Very pale dirty yellow, head reddish yellow,
mandibles dark red, teeth, scapes, anterior border of clypeus, and extreme
anterior angles of cheeks black, clothed with very sparse outstanding longer and
shorter yellow hairs and some fine very short decumbent yellow hairs. Sculpture
consisting of very fine reticulations, a little stronger on
head.
Head large, triangular, considerably broader behind than in front,
broadest a little before posterior angles, which are rounded and prominent,
posterior border excised, slightly sinuate on each side; mandibles massive,
strongly punctured and with transverse ridges, masticatory border armed with six
etc...
[[ worker ]] Of the same pale colour as the [[ soldier ]]. but only
the extreme anterior angle of clypens and cheeks blackish; the mandibles are
pale yellow with the teeth red. The sculpture and hairs are similar.
Head long, narrow, broader in front than behind, broadest a little
in front of sides of head, narrowed, rather sharply behind eyes to base; teeth
to mandibles somewhat more slender and sharper, carinae on clypeus a little more
pronounced; eyes more prominent. Thorax narrow and slender; pronotum more
narrowed to apex. Scale of petiole of similar shape, but a little narrower;
gaster and-legs of similar shape. Long. 10 - 12 mm.
Camponotus (Tanaemyrmex) gerberti
Species
Very like trispinosus but without the two shorter spines on the
mesonotum. The sculpture is different, and the species is also a little darker
in colour.
[[ worker ]]. Head: the sculpture is quite different; the disc is
smooth and shining, from the outer part of the smooth surface at sides
semicircular carinae run on each side along the cheeks, and from the posterior
part a few weaker carinae extend towards base of head, the space between these
and the posterior border of head being smooth and shining.
Thorax: the ridges on the pronotum are considerably less marked; the
mesonotum is smooth and shining and there are no spines present. The ridges on
the sides of the thorax are less marked; the dorsal surface and the declivity of
the epinotum are smooth and shining.
The spines on the pronotum are slightly longer and stronger, and
those of the epinotum, being of a different shape, being slightly shorter, and
projecting outwards then inwards in an even curve. Long. 5 mm.
Dodous bispinosus
Species
etc...
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%GREEN%Yep, you are right. Will fix in next release. We have to set up an OWL validator to catch stuff like this..... No wait! The element is empty. If it had content, that would have to be an infoItem. We are just using it as a place to hang the LSID of the taxonConcept. Terry and I talked about where to hang the LSID and this seemed appropriate. Have to check whether it is still OWL valid.... In general, I want to raise in Fremantle whether there are or should be best practices about where to squirrel LSIDs.-- Main.BobMorris - 01 Oct 2008 %ENDCOLOR%
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Regarding Patrick's comment about Bob's comment "Bob was of the idea that biological descriptions are statements of fact and are not intellectual property, therefore they cannot be licensed." The SPM needs to be capable of capturing the attribution data associated with the content and this attribution data can vary a lot. We can't just jump to the conclusion that all content is a fact and therefore unattributed. In science, I might think there is nothing that should be unattributed. This is different than "copyrighted". Content can be attributed without being copyrighted. For instance, there are plenty of authors of public domain content who get attribution. Can we address this area as "attribution" versus "intellectual property"? Some content attributions are in fact for copyright, others are not. How can the fact of a "some rights reserved" license like Creative Commons be included with the object? SPM should be capable to include all of the needed data elements to capture the attribution facts of the content. For the EOL's dataObject in its Transfer Schema, this has led to the use of new "agent" elements with roles of Source, Author, Project, and Publisher, combined with the elements dc:Rights, dcterms:RightsHolder, dcterms:bibliographicCitation, and dc:source. Also dc:description is used for the actual text content. We need to be able to include attribution facts in the SPM along with the scientific facts.-- Main.ChuckMiller - 01 Oct 2008
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I raised the question of how do we cite the descriptions. I see that each spm:SpeciesProfileModel has a spm:aboutTaxon which should ultimately reference a PublicationCitation with publishedIn. I can see that we can clearly cite the source of the taxon concept, but can we always infer that the publishedIn for the taxon is the same source of the description? What if I write a description on my own website, but cite person X's concept of the organism? Either way, it would be great to have a clear statement about the recommended way to infer the proper way to attribution statement for the description. This is also important for EOL and very important for those contributing content of their own.
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One thing that I would like to see included is the use of tn:rank in addition to tn:rankString. It is always good as a consumer to get content in the form of a controlled vocabulary rather than trying to reconcile varying rankStrings which mean the same thing.
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Note for Plazi: there are no line breaks in the text in this document. It seems that newlines in the descriptions do not represent line breaks (see #_Description_2_1). Is there some way to include line breaks - either using embedded escaped html or ensuring that newlines represent line breaks?
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-- Main.PatrickLeary - 30 Sep 2008
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I have been playing with this latest example a bit more today and have some new questions. The taxonConcepts use tc:hasInformation to point to the resource which describe the taxonConcept, but according to the standard tx:hasInformation should point to an infoItem, not a taxonConcept. So, is this invalid at this point?
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I also have a bit of a naive question, but one I would like to understand. SpeciesProfileModel contains two main elements which are of class taxonConcept and infoItem. The SPM element I suppose binds these two elements. But, if taxonConcept contains a hasInformation element, which is also an infoItem - couldn't we just have one RDF document which contains a bunch of taxonConcepts which have zero to many infoItems? In this latest example there are several SPM elements which only contain an aboutTaxon and it seems a bit unnecessary to have this extra SPM wrapper. I would be just as happy having a bunch of taxonConcepts, some of which contain infoItems.
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-- Main.PatrickLeary - 30 Sep 2008
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---+++ Clarification Needed
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* With proper handling of rank.
* hasContent now for each Description section, not each Paragraph in the Description
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-- Main.TerryCatapano - 23 Sep 2008
We'll need to modify our usage. Not crazy about it.
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[[http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept][see wiki page]]
*Deprecated* The taxonomic rank of this concept as a string. A string representation of the rank of this concept. It is highly recommended that the rank property be used along with this one unless the correct rank is not available in the rank vocabulary. No direct equivalent in TCS but is string version of /DataSet/TaxonConcepts/TaxonConcept/Rank. Requested by data suppliers. After discussions between a number of parties this property is considered to be deprecated. The rank of a TaxonConcept should be indicated by including a TaxonName of the appropriate rank in the hasName property even if the name object is empty apart from the rank.
-- Main.TerryCatapano - 23 Sep 2008
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---+++ Initial Example of 25 Aug 2008
lorem ipsum, quia dolor sit,
amet, consectetur, adipisci velit, sed quia non numquam eius modi
tempora\
incidunt, ut labore et dolore magnam aliquam quaerat voluptatem. Ut
enim ad minima veniam, quis nostrum exercitationem ullam corporis
susci\
pit laboriosam, nisi ut aliquid ex ea commodi consequatur? Quis autem
vel eum iure reprehenderit, qui in ea voluptate velit esse,
Aus Bus Plazi 2008
Species
-- Main.TerryCatapano - 25 Aug 2008
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---+++ Sample result of stylesheet conversion: 6 Sep 2008
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P. nigro-caeruleo-viridis, nitida et delicatule punctata; alis hyalinis.Female. Length 4 1 / 2 lines. Deep blue-green, with tints of purple in certain lights, particularly on the head, the clypeus with a central longitudinal ridge, its anterior margin slightly emarginate; the flagellum rufo-piceous beneath, the ocelli white. Thorax: the wings hyaline and brilliantly iridescent; the legs dark rufo-piceous with a bright purple tinge. Abdomen delicately punctured, the head and thorax more strongly so; the latter with a semicircular enclosed space at its base, which is smooth and shining.
Prosopis malachisis
Species
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Issues:
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Figs. 14, 35-36.
Worker description.- Head: Head rectangular; vertex planar or weakly
concave; frons ranging from shining, smooth with almost effaced reticulation to
shining and finely punctate-reticulate; pilosity of frons consisting of a few
short, thick, erect setae interspersed with short, appressed setulae. Eye
moderate, eye width 1-1.5x greatest width of antennal scape; (in full-face view)
eyes set at about midpoint of head capsule; (viewed in profile) eyes set around
midline of head capsule; eye elliptical, curvature of inner eye margin may be
more pronounced than that of its outer margin. Antennal segments 12; antennal
club three-segmented. Clypeal carinae indicated by multiple weak ridges;
etc...
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---+++ TaxonConcept - accordingToString property: 18 Sep 2008
Why can't you use the accordingToString property for TaxonConcept to solve this problem? Like this
Monomorium clarinodis Heterick
Species
Journal of Whatever, Vol. X, p. Y
-- Main.ChuckMiller - 18 Sep 2008
There's nothing wrong with this (well, nothing that isn't also a problem with the part of Terry's 17 Sep proposal. See below). However, it doesn't address the original, somewhat technical, problem Terry raised on Sep 6. That problem was essentially "How is it assured that the different elements of a !SpeciesProfileModel object all refer to the same taxon concept in the face of the fact that rdf:ID values must be unique in the document?" Terry's s proposed solution on Sep 17 is that rdf:ID not the right mechanism to solve the problem, since it is meant to identify an element in the document, not to identify stuff that the element is talking about. Instead, the appropriate thing to do is add an rdf:resource attribute and hang the LSID there. I think the main reason this is an issue at all is that an SPM can discuss other taxon concepts besides the one it is about. This use of rdf:resource seems to be the approach of most of the TDWG-based examples on the TDWG lsid resolver proxy service described at http://lsid.tdwg.org/.
I see these problems remaining:
* It's unclear to me that the current TDWG ontology definitions even allow for attributes to be hung on a the tc:TaxonConcept in the first place (or on any other defined rdf element for that matter...). I wonder if this means that while the proposed SPM is valid RDF, it may not be valid OWL.
* What semantics is imposed on rdf:resource whose value is the lsid of a tc:TaxonConcept that would insure that relevant string data in the resolved !TaxonConcept is in any way related (preferably is the same as) the string data offered in the document. Unless the document string data were generated by _resolving_ the lsid (and maybe even then if the TC object is returned in the lsid metadata and not its data) there can be no such guarantee. Indeed, the Hymenoptera Name Server lsids return everything in the metadata. The lsid might resolve to something that is not even meaningfully the same as the one described by the string data. I raised that problem when the original Sep 6 issue was raised.
-- Main.BobMorris - 19 Sep 2008
---++ Namespace termination
It is pretty important to terminate namespace values with either '/' or '#'. Although failing to do so is valid RDF/XML serialization, it can result in ambiguity in the triple form of the RDF, wherein local name is concatenated with namespace to form resource names. Here's a good NamespaceTermination example from Adobe's XMP manual.
%SEARCH{"%TOPIC%" excludetopic="%TOPIC%" header="---++Linking Topics" format=" * $topic" nosearch="on" nototal="on" }%
---++ Deprecation of tc:rankString
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anteromedian clypeal margin broadly convex; paraclypeal setae short and
thickened, not reaching basal margin of closed mandibles; posteromedian clypeal
margin approximately level with antennal fossae. Anterior tentorial pits
situated nearer antennal fossae than mandibular insertions. Frontal lobes
straight, parallel. Psammophore absent. Palp formula 5,3. Mandibular teeth five;
mandibles triangular and mainly smooth (weakly striate basally); masticatory
margin of mandibles approximately vertical or weakly oblique; basal tooth
approximately same size as t4 (five teeth present).Mesosoma: Promesonotum
shining and microreticulate, microreticulation reduced on humeri, or, shining
and smooth on dorsum, lower mesopleuron strongly punctate; (viewed in profile)
promesonotum broadly convex, or, anterior promesonotum smoothly rounded,
thereafter more-orless flattened, promesonotum on same plane as propodeum;
promesonotal setae very variable, from one or two to up to a dozen; standing
promesonotal setae consisting of short, erect or semi-erect bristles; appressed
promesonotal setulae well-spaced over entire promesonotum. Metanotal groove
vestigial. Propodeum with reduced sculpture, generally smooth dorsally,
metapleuron punctate; propodeal dorsum flat throughout most of its length;
propodeum smoothly rounded or with indistinct angle, but dorsal and declivitous
faces separated when seen in profile; standing propodeal setae absent; appressed
propodeal setulae very sparse or absent; propodeal spiracle nearer declivitous
face of propodeum than metanotal groove. Vestibule of propodeal spiracle absent
or not visible. Propodeal lobes present as vestigial flanges or small strips of
cuticle only.Petiole and postpetiole: Petiolar spiracle laterodorsal and
situated well anteriad of petiolar node; node (viewed in profile) cuneate,
vertex rounded; appearance of node shining and faintly microreticulate; ratio of
greatest node breadth (viewed from front) to greatest node width (viewed in
profile) between 4:3 and1:1; anteroventral petiolar process absent or vestigial;
ventral petiolar lobe absent; height ratio of petiole to postpetiole between 4:3
and 1:1; height -length ratio of postpetiole about 1:1; postpetiole shining,
with vestigial sculpture; postpetiolar sternite not depressed at midpoint, its
anterior end an inconspicuous lip or small carina.Gaster: Pilosity of first
gastral tergite consisting of well-spaced, short, thick, erect setae
interspersed with minute, appressed setulae.General characters: Color from
orange or yellowish with gaster light brown, through to uniform chocolate.
Worker caste monomorphic.Holotype worker measurements: HML 1.55 HL 0.53 HW 0.44
CeI 83 SL 0.40 SI 91 PW 0.32.Other worker measurements: HML 1.22-1.57 HL
0.45-0.55 HW 0.35-0.47 CeI 78-87 SL 0.32-0.43 SI 90-97 PW 0.26-0.35 (n=20).Queen
description.- Head: Head rectangular; vertex always planar; frons shining and
smooth except for piliferous pits; pilosity of frons a mixture of well-spaced,
distinctly longer erect and semi-erect setae interspersed with shorter setae or
setulae, which are decumbent or appressed, longer setae thickest on vertex. Eye
elliptical, curvature of inner eye margin may be more pronounced than that of
its outer margin; (in full-face view) eyes set at about midpoint of head
capsule; (viewed in profile) eyes set posteriad of midline of head
capsule.Mesosoma: Mesoscutum broadly convex anteriad, convexity reduced
posteriad; pronotum, mesoscutum and mesopleuron shining and mainly smooth,
vestigial striolae, if present, confined to anterior katepisternum; length
-width ratio of mesoscutum and scutellum combined between 2:1 and 3:2; axillae
narrowly separated (i.e., less than width of one axilla); standing
pronotal/mesoscutal setae consisting of well-spaced, incurved, erect and
semi-erect setae only; appressed pronotal, mescoscutal and mesopleural setulae
few, mainly on dorsum of pronotum and mesoscutum. Propodeum shining and
microreticulate; propodeum distinctly angulate, propodeal angles produced as
short denticles; propodeal dorsum sloping posteriad, and depressed between
raised propodeal angles; standing propodeal setae absent; appressed propodeal
setulae very sparse or absent; propodeal spiracle equidistant from metanotal
groove and declivitous face of propodeum. Propodeal lobes present as vestigial
flanges only, or absent.Wing: Wing not seen (queen dealated).Petiole and
postpetiole: Petiolar spiracle lateral and situated well anteriad of petiolar
node; node (viewed in profile) cuneate, vertex tapered; appearance of node
shining and microreticulate; ratio of greatest node breadth (viewed from front)
to greatest node width (viewed in profile) about 4:3; anteroventral petiolar
process absent or vestigial; height ratio of petiole to postpetiole about 1:1;
height -length ratio of postpetiole between 4:3 and 1:1; postpetiole shining and
microreticulate; postpetiolar sternite not depressed, in form of narrow,
rectangular projection.Gaster: Pilosity of first gastral tergite consisting of
well-spaced, short, thick, erect setae interspersed with minute, appressed
setulae.General characters: Color brownish-yellow, gaster darker. Brachypterous
alates not seen. Ergatoid or worker-female intercastes not seen.Queen
measurements: HML 2.29 HL 0.66 HW 0.61 CeI 92 SL 0.52 SI 85 PW 0.52
(n=1).
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P. nigro-caeruleo-viridis, nitida et delicatule punctata; alis hyalinis.Female. Length 4 1 / 2 lines. Deep blue-green, with tints of purple in certain lights, particularly on the head, the clypeus with a central longitudinal ridge, its anterior margin slightly emarginate; the flagellum rufo-piceous beneath, the ocelli white. Thorax: the wings hyaline and brilliantly iridescent; the legs dark rufo-piceous with a bright purple tinge. Abdomen delicately punctured, the head and thorax more strongly so; the latter with a semicircular enclosed space at its base, which is smooth and shining.
Prosopis malachisis
Species
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-- Main.TerryCatapano - 25 Aug 2008
---++ TDWG ontology defects obstructing SPM deployment
---+++ !TaxonConcept
The !TaxonConcept RDF at http://rs.tdwg.org/ontology/voc/TaxonConcept does not appear to support any property for the publication in which the accordingTo may have appeared. Discussion should cross reference the TDWG [[http://rs.tdwg.org/ontology/voc/TaxonConcept !TaxonConcept DiscussionPage]]
-- Main.BobMorris - 25 Aug 2008
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Place holder for Plazi EOL project on SPM
-- Main.EamonnOTuama - 30 Jul 2008
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The !TaxonConcept RDF at http://rs.tdwg.org/ontology/voc/TaxonConcept does not appear to support any property for the publication in which the accordingTo may have appeared. Discussion should cross reference the TDWG [[http://rs.tdwg.org/ontology/voc/TaxonConcept !TaxonConcept DiscussionPage]] for
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