What licenses should be placed on an ontology? Is it just a document? Can/should/must a license be applied that is independent of serialization?

Are there parts that should not be allowed to be change by other than the licensor? See for example http://human-phenotype-ontology.github.io/license.html

Does this issue belong in this project?

SKOS? Table?

current instances for predefined use of object of hasScope.

Pehaps below is and example SPARQL axiom lending meaning to the "any" scopes, something like:

CONSTRUCT { ?d tmt:hasScope tmt:female .
?d tmt:hasScope tmt:male . }
FROM
WHERE { ?d rdf:type tmt:Description .
?d tmt:hasScope tmt:anySex }

If someone can post something better, or can cite similar use of SPARQL, please add to this issue.

A number of terms emitted by GGS are put in the dwc namespace but are in fact not in Darwin Core. The currently known ones are
HigherTaxonomySource
and others
These are actually provenance terms and belong in a provenance vocabulary if not existing elsewhere.

There may be other misattributed terms in GGS output. If they are not provenance terms, make a separate issue(s)

Provenance is a major issue in data management, and Plazi should follow standards, especially such as may be discussed in TDWG

@tcatapano @punkish @mguidoti @retog @mguidoti
we need to develop a "plazi vocabulary" to assure we can communicate across our various projects, import to GBIF, create "clean" RDF, etc.

What is the proper process recommended?

• use this plazi/ontologies repo
• add all the projects and local lists, vocabularies
• describe the goal
• describe the subprojects to get there, eg.
  • described what we want the goal is
  • create github PlaziVocabulary
  • add all the various lists, etc so we have an overview
  • decide on a format how we want to document and map all the vocabularies
  • map the part-vocabularies
  • describe all the terms
  • map the mapped plazi vocabulary with DWC and other existing vocabularies
  • define the elements that do not map
  • create a reference vocabulary that allows to cite the terms

At that stage, I would restrain from building an ontology, since we do not have the resources, and it is at least for me now clear, whether we need one right now.?

I would like to see that we have this vocabulary ready by October 15 for our TDWG presentations.

some of the existing vocabularies:

1. Plazi article: https://tb.plazi.org/GgServer/dioStats/fields or just add ?format=JSON
2. Plazi treatments: https://tb.plazi.org/GgServer/srsStats/fields.
3. Mapping NMBE-RDF ontologies https://docs.google.com/spreadsheets/d/1OeI8zfbzFB27FGos_l0snwaBuqNEaZ3d1FByjvkVO9E/edit#gid=816562804
4. TB: https://hackmd.io/IcBwiUG8TtiQ-Vd0oY_-mg
5. Zenodeo
6. RDF terms by Reto
7. Documentations and Vocabularies
8. Documentations, Glossaries, Ontologies and Vocabularies
9. GoldenGate Glossary
10. Plazi Glossary

@punkish please add Zenodeo terms to Plazi vocabulary https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436

Currently, we are having two different RDF representations of treatments.

For example for the treatment 03CB87C52324FFE6FCDE9030FA24F97E we provide the following two representations (in RDF Turtle for readability).

@prefix ns0: <http://plazi.org/vocab/treatment#> .
@prefix dc11: <http://purl.org/dc/elements/1.1/> .
@prefix bibo: <http://purl.org/ontology/bibo/> .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:treatsTaxonName <http://taxon-name.plazi.org/id/Animalia/Galearis_spectabilis> ;
  dc11:creator "Jarvis, Charlie" ;
  ns0:publishedIn <http://dx.doi.org/10.5281/zenodo.250878> ;
  ns0:citesTaxonName <http://tb.plazi.org/GgServer/lodRdf/Orchis_spectabilis> .

<http://dx.doi.org/10.5281/zenodo.250878>
  dc11:title "pp 705 - 708 in: Order out of Chaos" ;
  dc11:creator "Jarvis, Charlie" ;
  a <http://purl.org/spar/fabio/BookSection> ;
  dc11:date "2007" ;
  bibo:startPage "705" ;
  bibo:endPage "708" .

@prefix ns0: <http://plazi.org/vocab/treatment#> .
@prefix ns1: <http://purl.org/spar/cito/> .
@prefix ns2: <http://rs.tdwg.org/ontology/voc/> .
@prefix dc11: <http://purl.org/dc/elements/1.1/> .
@prefix ns3: <http://rs.tdwg.org/dwc/terms/> .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E> ;
  ns0:publishedIn <http://dx.doi.org/10.5281/zenodo.250878> ;
  ns1:cites "Orchis spectabilis Linnaeus" ;
  ns2:SpeciesProfileModelhasInformation <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_1>, <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_2>, <http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_3> .

<http://dx.doi.org/10.5281/zenodo.250878>
  dc11:title "pp 705 - 708 in: Order out of Chaos" ;
  dc11:creator "Jarvis, Charlie" .

<http://taxon-concept.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E>
  a <http://filteredpush.org/ontologies/oa/dwcFP#Taxon> ;
  ns3:LSID-IPNI "urn:lsid:ipni.org:names:1009442-2" ;
  ns3:authorityName "(L.) Raf." ;
  ns3:authorityPageNumber "1837" ;
  ns3:box "[1030,1313,1719,1741]" ;
  ns3:class "Liliopsida" ;
  ns3:family "Orchidaceae" ;
  ns3:genus "Galearis" ;
  ns3:kingdom "Plantae" ;
  ns3:order "Asparagales" ;
  ns3:pageId "2" ;
  ns3:pageNumber "707" ;
  ns3:phylum "Tracheophyta" ;
  ns3:rank "species" ;
  ns3:species "spectabilis" .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_1>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent "   Orchis spectabilisLinnaeus, Species Plantarum2: 943- 1753." .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_2>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent " “ Habitatin Virginia. D. Gronovius.” RCN: 6832." .

<http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E#section_3>
  a <spm:InfoItem> ;
  ns2:SpeciesProfileModelhasContent " Lectotype (Sheviak in Cafferty & Jarvis in Taxon48: 49. 1999): Clayton s.n.,Herb. Linn. No. 1054.44 (LINN)." .

The first graph is available when dereferencing http://treatment.plazi.org/id/03CB87C52324FFE6FCDE9030FA24F97E with an appropriate accept-header as well when dereferencing http://tb.plazi.org/GgServer/lodRdf/03CB87C52324FFE6FCDE9030FA24F97E. The second Graph is available at http://tb.plazi.org/GgServer/rdf/03CB87C52324FFE6FCDE9030FA24F97E.

I suggest serving a unified RDF representation describing all the information we have about a treatment in a way that is accessible to all users of our RDF data and which aims for wide compliance with Data on the Web Best Practices.

Differences in the expressed content

One version contains more literal content of the treatment in the form of "InfoItems" the other version contains more explicit information about synonymity.

example

Treatment 03ACBF18FFD61B34FF31FB52FD04ED5B "deprecates" Sadayoshia_acroporae_Macpherson_2010 and defines adayoshia_aludra_Macpherson_2012 according to the lodRdf version:

<http://treatment.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/Animalia/Sadayoshia_aludra_Macpherson_2012> ;
  ns0:deprecates <http://taxon-concept.plazi.org/id/Animalia/Sadayoshia_acroporae_Macpherson_2010> ;
  ns1:cites <http://dx.doi.org/10.5281/zenodo.214647>, <http://dx.doi.org/10.5281/zenodo.214650> .
  ...

The other rdf version states in regard to these two names:

<http://treatment.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://plazi.org/vocab/treatment#Treatment> ;
  ns0:definesTaxonConcept <http://taxon-concept.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B> ;
  ns1:cites "Sadayoshia acroporae Macpherson & Baba 2010 : 418" ;
 ...

<http://taxon-concept.plazi.org/id/03ACBF18FFD61B34FF31FB52FD04ED5B>
  a <http://filteredpush.org/ontologies/oa/dwcFP#Taxon> ;
...
  ns4:rank "species" ;
  ns4:species "aludra" ;
  ns4:status "n. sp." .

@myrmoteras Shall we have a meeting tomorrow at 6 PM CEST?

###  http://dx.doi.org/http://dx.doi.org/10.3897/zookeys.454.7269
<http://dx.doi.org/http://dx.doi.org/10.3897/zookeys.454.7269> rdf:type owl:NamedIndividual ,
                                                                        <fabio:JournalArticle> ;
                                                               dc:creator "Huang, Sunbin" ,
                                                                          "Tian, Mingyi" ,
                                                                          "Yin, Haomin" ;
                                                               dc:date "2014" ;
                                                               dc:title "Du'an Karst of Guangxi: a kingdom of the cavernicolous genus Dongodytes Deuve (Coleoptera, Carabidae, Trechinae)" ;
                                                               bibo:endPage "107" ;
                                                               bibo:journal "ZooKeys" ;
                                                               bibo:startPage "69" ;
                                                               bibo:volume "454" .

bibo:startPage and bibo:endPage seem to be undefined, at least in the OWL file which is in the "ontologies" subdirectory

The XSLT seems to generate statements like

http://taxon-concept.plazi.org/id/1A21E9DA831195C4950E2AB084250E05

http://taxon-concept.plazi.org/id/1A21E9DA831195C4950E2AB084250E05 rdf:type owl:NamedIndividual ,
dwcFP:TaxonConcept ;
dwc:authority "Tian, 2011" ;
dwc:authorityName "Tian" ;
dwc:authorityYear "2011" ;
dwc:class "Insecta" ;
dwc:family "Carabidae" ;
dwc:genus "Dongodytes" ;
dwc:higherTaxonomySource "CoL" ;
dwc:kingdom "Animalia" ;
dwc:lsidName "Dongodytes deharvengi" ;
dwc:order "Coleoptera" ;
dwc:pageId "9" ;
dwc:pageNumber "78" ;
dwc:phylum "Arthropoda" ;
dwc:rank "species" ;
dwc:species "deharvengi" ;
dwc:subGenus "Dongodytodes" .

Note the dwcFP:TaxonConcept. This does not exist in dwcFP in my opinion. In my opinion it should be changed to dwcFP:Taxon.

These are generated from the GG specific attributes in the source XML for material citations

To group multiple material_examined

should we explicity urge, recommend against, or not mention the use of both sides of a pair of inverse properties, e.g. BOTH of
sdd:definedBy and
sdd:definesTaxonConcept

Pro: Might make it easier for application writers with no access to reasoners to map from on to another
Con: Data errors could lead to unintended errors in a triple store

Per Guido: Some ideas, tbd:

definesConcept e.g., "spec. nov."
augmentsConcept e.g. "Aus bus Agosti 2015......"
subordinatesConcept e.g., "syn. nov.; comb. nov."
citesAsSubordinateConcept
citesAsRelatedConcept

Shall we add the openBiodDiv ontology terms to our vocabulary google XLS?

http://openbiodiv.net/ontology

via @tcatapano
the terms and their definitions in the taxonomic_nomenclatural_status_terms.owl ontology by Paul Morris as basis for further discussions

nomenclatorial terms

@myrmoteras can you please add the terms from https://docs.google.com/spreadsheets/d/1OeI8zfbzFB27FGos_l0snwaBuqNEaZ3d1FByjvkVO9E/edit#gid=816562804 to column M in https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436

https://www.tdwg.org/conferences/2021/session-list/

SYM12 Connecting biodiversity data with knowledge graphs
Session Type: Symposium (unsolicited presentations considered)

Organizers: Roderic D.M. Page, University of Glasgow, Glasgow, UK; Franck Michel, University Côte d'Azur, CNRS, Inria, Sophia Antipolis, France

Linking biodiversity data together is an implicit goal of many initiatives in biodiversity informatics. Taxonomic databases were early adopters of the Resource Description Framework (RDF), a building block for the Semantic Web. From 2006 onwards they were serving up millions of taxonomic names in RDF, each with a globally unique identifier such as Life Science Identifiers (LSIDs), hence the field was seemingly ripe for a "biodiversity knowledge graph", a network of interconnected data that we could use to discover links between taxa, their names, the relevant publications, specimens, occurrences, traits, phenotypes, DNA sequences, and the people whose work enabled the creation of that knowledge.

However the biodiversity knowledge graph did not spontaneously assemble itself, suggesting that more work needs to be done before the knowledge graph becomes a key tool for integrating and exploring biodiversity data. This session will explore progress and prospects for constructing and exploiting biodiversity knowledge graphs, whether centered around broader efforts such as Wikidata or DBpedia, or more focussed on domain-specific initiatives such as Ozymandias and OpenBiodiv. In addition to these case studies, speakers in the session will explore the relationships between TDWG standards, data formats such as JSON-LD, markup vocabularies such as Bioschemas and the role nanopubs can play in disseminating and linking biodiversity knowledge. The session will also welcome presentations on the joint exploitation and cross-fertilization of biodiversity knowledge graphs and more "traditional" biodiversity data sources.

see: https://github.com/plazi/TreatmentOntologies/blob/material_modelling/test/21401.n3

In order to make clear the distinction between the material citation and the actual material, and to be able to make assertions about both, I've introduced a a new property for treatment, hasMaterialCitation, which has as its object a materialCitation, typed as a cito:CitationAct, which has the property hasCitedEntity whose object is a Material (e.g., the actual specimen).

@pdatascience: what do you think?

@mguidoti please add the terms from the HackMD https://hackmd.io/IcBwiUG8TtiQ-Vd0oY_-mg to column L in https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436

https://openbiodiv.net/ontologies

how can we use this ontologies, eg for terms like taxonomicConcept, treatmentCitation, etc?

see also

Hi Lyubo and Teodor
Where is the openbiodiv ontology? We whould like to use it but we can de-reference the terms, eg https://openbiodiv.net/ScientificName

Or taxonomicConcept.

Thanks for a hint

Donat

Determine how much of Openbiodiv-O can and should be used.

https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0174-5

@gsautter can you please complete the XML terms used in GGI and TreatmentBank to column B?
https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436

You can also let me know, so I can give you a hand.

Make a small maven pom file that will attempt to download the required dependencies into a convenient local directory for examination during development

Here is the Google Drive XLS that we can use as starting point. It is from our Arcadia sprint and which led to Puneets Zenodeo vocabulary.

https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436

@retog @punkish @tcatapano @mguidoti can we agree on this to add all the terms from our various projects?

presently ontologies/ holds entirely things that we use in treatment.owl but we do not maintain. I propose:

1. (Terry) Remove them all and consider adding a text file "dependencies.txt" with a list of the dependencies
2. (Terry) Move treatment,owl into ontologies/ and in future put only things we maintain there.
3. (Bob) Put an appropriate DwC owl model in ontologies/

@retog can you please add in column K https://docs.google.com/spreadsheets/d/12hEiMS1HjmeKMki23-EzBauPvf7zP5URB-YSIcPZTHI/edit#gid=1415791436 the RDF terms?

in test/21401.n3 and test/Szero_full.n3 geography is an attribute of a Material, but it should be an attribute of a CollectionEvent

EXTERNAL SENDER

Hi Lyubo,

Not sure this will be helpful, but see:

https://github.com/plazi/ontologies/blob/master/treatment.owl

This seems to be used by the rdf files under

https://github.com/plazi/treatments-rdf/blob/main/data.

which are used by synospecies.

I extracted all the "trt:" terms actually in the ttl files in under the data repo and came up with this list of unique terms:

augmentsTaxonConcept
citesTaxonName
definesTaxonConcept
deprecates
gbifOccurrenceId
gbifSpecimenId
hasParentName
hasTaxonName
publishedIn
treatsTaxonName

I remember also there being an provisional OWL ontology for nomenclatural terms developed (I think) by Paul Morris way back. A copy is in the Plazi ontologies repo:

https://github.com/plazi/ontologies/blob/master/ontologies/taxonomic_nomenclatural_status_terms.owl

Please let me know if this helps. Im sure Reto knows much more and better.

/Terry

On Tue, May 23, 2023 at 12:54 AM Lyubomir Penev <[email protected]> wrote:

Hi Donat and Terry,

II have a question, please. Are you aware about ontologies that models the nomenclatural acts, e.g. of the type Taxon concept ID (Aus bus) is JuniorSynonym of Taxon concept ID (Bus Cus). I am especially interested in the predicate, and especially if it is available through an ontology API delivering IDs and http links to each term or relationships?

I would be thankful if you send me a hint, if such exists. For example what kind of ontology do you use for Synospecies?

Best regards,

Lyubo

---

Lyubomir Penev
ORCID: http://orcid.org/0000-0002-2186-5033

An example treatment:

http://treatment.plazi.org/id/0610DE63-4A62-5801-C11B-0C8AD642A55A

FlyBase vocabularies:

http://flybase.org/static_pages/termlink/termlink.html

Cant seem to find the actual formal vocabulary/ontology files, however

Consider test/Szero_full.n3, which has
http://treatment.plazi.org/id/31F96F41E3E002BD88985A4F3A20E45A a tmt:Treatment ;
.....
tmt:publishedIn doi:10.1371/journal.pone.0001787 ;
....

and consider a URI constructed to uniquely resolve to the text string that comprises the portion of http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001787 that is the text of the treat with URI http://treatment.plazi.org/id/31F96F41E3E002BD88985A4F3A20E45A

Do we need to model a relation between these two? Does the string URI deserve to be typed as a tmt:Treatment?

zootaxa.5303.1.1