index nanopubs with species interaction claims on BDJ via KnowledgePixels #923

jhpoelen · 2023-09-22T14:35:22Z

via https://bdj.pensoft.net/nanopublications

jhpoelen · 2023-09-22T14:36:19Z

fyi @tkuhn - any ideas to help index this?

jhpoelen · 2023-09-22T14:37:54Z

https://np.petapico.org/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU

@prefix this: <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> .
@prefix sub: <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation> ;
    rdfs:comment "Wolf (Canis lupus) predation and scavenging of reintroduced bison (Bison bison): a hallmark of ecological restoration to boreal food webs" ;
    <https://w3id.org/biolink/vocab/object> sub:objtaxon ;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002439> ;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon ;
    <https://w3id.org/kpxl/biodiv/terms/hasSubjectLifeCycleStage> <http://purl.obolibrary.org/obo/UBERON_0018241> .
  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/2169/taxon/9901> .
  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/QLXL> .
}
sub:provenance {
  sub:assertion prov:wasDerivedFrom <https://doi.org/10.1007/s10344-023-01676-0> .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCjDGQCS1S+SRnERDuYDXOugdYUP0efEquHJEEHAbU/uLzBVlga89zqrNPCS7fBE6lArBUWEmT8eLKdMapyqvAzI1J3jUWTMhDJF+XFBkUiuiFfNSc4vJJcmi0yujtnuzXsRIG202jyaP4f5ULoskFwaZOSBZJfiE0dsB3D7DTIAQIDAQAB" ;
    npx:hasSignature "BmxFhIUMaljf5MGd6ETv/dTclruWtt0knKiiU9wJPKaq1G3ZfTloNVZB6AckOoKivlQDVr8D8qas4enqbRGhWYLV2se7YMsiMg1lTB09WndovUXp9+5lRIy1s0z1nKF4VqBYEfMNuujtYPyQ8X+cDgqpSjZecrX3iqlBcYlGTD0=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2023-09-15T08:54:31.806Z"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-1267-0234 ;
    dct:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
    npx:hasNanopubType <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub> ;
    npx:introduces sub:association ;
    rdfs:label "Canis lupus Linnaeus, 1758 (species) - preys on - Bison bison (species)" ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAcTpoh5Ra0ssqmcpOgWdaZ_YiPE6demO6cpw-2RvSNs8> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> , <http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0> .
  <https://www.checklistbank.org/dataset/2169/taxon/9901> nt:hasLabelFromApi "Bison bison (species)" .
  <https://www.checklistbank.org/dataset/9880/taxon/QLXL> nt:hasLabelFromApi "Canis lupus Linnaeus, 1758 (species)" .
}

jhpoelen · 2023-09-22T14:48:32Z

See related publications -

https://www.globalbioticinteractions.org/?interactionType=eatenBy&sourceTaxon=Bison%20bison&targetTaxon=Canis%20lupus

and via https://www.globalbioticinteractions.org/references.html?interactionType=eatenBy&sourceTaxon=Bison%20bison&targetTaxon=Canis%20lupus

Many of which are included in iNaturalist https://globalbioticinteractions.org/datasets

available via https://depot.globalbioticinteractions.org/reviews/globalbioticinteractions/inaturalist/nanopub.trig.gz .

jhpoelen · 2023-09-22T14:59:06Z

Here's an example from the existing inaturalist nanopub collection:

curl "https://depot.globalbioticinteractions.org/reviews/globalbioticinteractions/inaturalist/nanopub.trig.gz" | gunzip | grep "28845843" | tee result.trig

with result.trig being:

@prefix this: <http://purl.org/np/RA3-Hm3EHGkwsYBExRQsIreNRnA4cu9hlFTc7NIAWc-o0> . @prefix sub: <http://purl.org/np/RA3-Hm3EHGkwsYBExRQsIreNRnA4cu9hlFTc7NIAWc-o0#> . @prefix np: <http://www.nanopub.org/nschema#> . @prefix dcterms: <http://purl.org/dc/terms/> . @prefix prov: <http://www.w3.org/ns/prov#> . @prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .  sub:Head {   this: np:hasAssertion sub:Assertion;     np:hasProvenance sub:Provenance;     np:hasPublicationInfo sub:Pubinfo;     a np:Nanopublication . }  sub:Assertion {   sub:Interaction obo:RO_0000057 sub:Organism_1, sub:Organism_2;     a obo:GO_0044419;     geo:latitude "44.883776052"^^xsd:decimal;     geo:longitude "-110.1556417747"^^xsd:decimal;     prov:atTime "2019-06-18T01:30:00Z"^^xsd:dateTime .      sub:Organism_1 obo:RO_0002439 sub:Organism_2;     a <https://inaturalist.org/taxa/42048>;     rdfs:label "Canis lupus" .      sub:Organism_2 a <https://inaturalist.org/taxa/123788>;     rdfs:label "Bison bison bison" . }  sub:Provenance {   sub:Assertion prov:wasDerivedFrom sub:Study .      sub:Study dcterms:bibliographicCitation "Jon Brooks. 2019. Canis lupus interaction-&gt;preyed on Bison bison bison. iNaturalist.org. Accessed at &lt;https://www.inaturalist.org/observations/28845843&gt; on 19 Sep 2023." . }  sub:Pubinfo {   this: dcterms:license <https://creativecommons.org/licenses/by/4.0/>;     pav:createdBy <https://doi.org/10.5281/zenodo.998263>;     prov:wasDerivedFrom <https://github.com/globalbioticinteractions/inaturalist> .      <https://github.com/globalbioticinteractions/inaturalist> dcterms:bibliographicCitation       "http://iNaturalist.org is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world." . }

with associated iNaturalist observation at https://www.inaturalist.org/observations/28845843

With GloBI's view -

jhpoelen · 2023-09-25T19:27:47Z

Another example of GloBI generated nanopubs -

<https://depot.globalbioticinteractions.org/reviews/FloraVincent/DIDB/nanopub-sample.trig> <http://purl.org/pav/hasVersion> <hash://sha256/021a51280545d8f92fe423ae8c86279e36b0b3d773a25d43a30e0b759f95cb5a> .

FloraVincent-DIDB-sample.trig.txt

tkuhn · 2023-09-26T07:30:42Z

With "index" you mean to use these nanopublications in tools like https://www.globalbioticinteractions.org? Or the other way round, to feed the nanopublications you are already generating into the nanopub ecosystem? Or both? :)

jhpoelen · 2023-09-26T12:43:30Z

Ideally both.

And, to get started, I'd want to be able to find nanopublications in Pensoft associated resources that make statements involving species interactions (or biotic interactions).

In other words:

query X to retrieve Pensoft Associated Resources
version Pensoft associated resources (nanopubs?)
add versioned resources to GloBI index
query for X in GloBI to find Pensoft associated resources

jhpoelen · 2023-09-26T14:50:41Z

@tkuhn curious to hear your thoughts on the GloBI<>Pensoft Nanopub integration proposal .

tkuhn · 2023-09-27T12:25:25Z

Yes, makes sense to first focus on the Nanopub>GloBI direction.

You can, for example, get all taxon-taxon relations according to the templates used at Pensoft with this API call (add .csv or .json to get machine-friendly formats): https://grlc.petapico.org/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs

It executes in the back this SPARQL query: https://github.com/knowledgepixels/bdj-nanopub-api/blob/main/get-taxontaxon-nanopubs.rq

Does that match what you are looking for? We can adjust the query to get out what you need, basically.

That would cover points 1 and 2 in your list, as nanopublications are already versioned with their hash-based Trusty URI (unless the GloBI index requires a different kind of versioning).

The above API call returns all nanopublications that match the template as defined for the Pensoft pilot. But these nanopublications are otherwise not necessarily associated with Pensoft. Some will be reviewed and formally accepted at Pensoft (coming soon), others might be associated with upcoming submissions there, and others might have no link to Pensoft other than using the same or similar nanopub structure.

jhpoelen · 2023-09-27T14:22:51Z

@tkuhn thanks for your prompt reply and detailed examples.

Am eager to get this integration up and running.

I tried the api call https://grlc.petapico.org/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs in a web browser

and got a timeout. Is that expected?

tkuhn · 2023-09-27T14:26:32Z

Yeah, sorry, the petapico.org server keeps misbehaving. I should have given you this one: https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs

jhpoelen · 2023-09-27T14:27:47Z

@tkuhn thanks! I got some results now -

…nteractions/globalbioticinteractions#923

jhpoelen · 2023-09-27T14:43:21Z

A first pass at index configuration is available via https://github.com/globalbioticinteractions/knowledgepixels .

For some reason, the url https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs.csv works 200/OK in curl / web browser. However, when using elton's http client, a 500 server error is generated.

What can I do to help troubleshoot this likely http request header issue?

jhpoelen · 2023-09-27T16:07:25Z

See related issue globalbioticinteractions/knowledgepixels#1 .

tkuhn · 2023-09-29T10:52:36Z

Hmm, I don't know what could be the reason that the elton client is getting a 500 error.

I am seeing some KeyError: 'HTTP_ACCEPT' in the logs. Not sure it's related to this, but might be.

Can you maybe see the precise request with HTTP headers that elton is sending?

@tkuhn

…nteractions#923 (comment) ; fyi @tkuhn

jhpoelen · 2023-09-29T11:30:46Z

As far as I can tell, the request header is empty -

As obtained via

globalbioticinteractions/eol-globi-resource-remote/src/test/java/org/eol/globi/util/ResourceServiceHTTPIT.java

Line 14 in f215052

    
           service.retrieve(URI.create("https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs.csv"));

.

jhpoelen · 2023-11-02T19:03:17Z

@tkuhn any update on why knowledgepixel crashes on retrieval of content via Elton? https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs.csv

As far as I can tell, Elton works just fine with non-knowledgepixel servers.

I suspect a server-side processing error of sorts.

Can you confirm?

tkuhn · 2023-11-03T09:24:53Z

It seems to be the occurring when the Accept header is missing. Is it possible to add ´Accept: */*´ on your side?

On my side this is based on the third-party tool grlc, and I am not sure how easy it would be to change this behavior...

jhpoelen · 2023-11-03T11:09:33Z

@tkuhn Thanks for having a look and I'll make an effort to add the accept header. Perhaps worth a bug report for grlc ? Seems weird to have things crash on a missing Accept header.

…tkuhn

…tkuhn

jhpoelen · 2023-11-03T14:41:12Z

related grlc issue - CLARIAH/grlc#402 .

jhpoelen · 2023-11-10T00:38:18Z

Now, with elton v0.12.12, I can do -

elton pull globalbioticinteractions/knowledgepixels\
 && elton interactions globalbioticinteractions/knowledgepixels\

to produce a table (abbreviated for display)

sourceTaxonId	sourceTaxonName	interactionTypeId	interactionTypeName	targetTaxonId	targetTaxonName	referenceUrl	referenceCitation
https://www.checklistbank.org/dataset/9880/taxon/QLXL		http://purl.obolibrary.org/obo/RO_0002439	preysOn	https://www.checklistbank.org/dataset/2169/taxon/9901		http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU	Canis lupus Linnaeus, 1758 (species) - preys on - Bison bison (species)
https://www.checklistbank.org/dataset/9880/taxon/QLXL		http://purl.obolibrary.org/obo/RO_0002470	eats	https://www.checklistbank.org/dataset/9880/taxon/48NBQ		http://purl.org/np/RALX2suiPKea3pm65RjS97EL6k9iY1Jew_mb30hO5Zjv0	Canis lupus Linnaeus, 1758 (species) - eats - Odocoileus virginianus (Zimmermann, 1780) (species)

jhpoelen · 2023-11-10T00:44:34Z

and, following the nanopub . . .
https://np.petapico.org/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU

@tkuhn very cool!

via

curl "https://np.petapico.org/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU.nq"

got

<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://www.nanopub.org/nschema#hasAssertion> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#Head> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://www.nanopub.org/nschema#hasProvenance> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#provenance> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#Head> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://www.nanopub.org/nschema#hasPublicationInfo> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#Head> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.nanopub.org/nschema#Nanopublication> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#Head> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <http://www.w3.org/2000/01/rdf-schema#comment> "Wolf (Canis lupus) predation and scavenging of reintroduced bison (Bison bison): a hallmark of ecological restoration to boreal food webs" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <https://w3id.org/biolink/vocab/object> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#objtaxon> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002439> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <https://w3id.org/biolink/vocab/subject> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#subjtaxon> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <https://w3id.org/kpxl/biodiv/terms/hasSubjectLifeCycleStage> <http://purl.obolibrary.org/obo/UBERON_0018241> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#objtaxon> <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/2169/taxon/9901> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#subjtaxon> <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/QLXL> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#assertion> <http://www.w3.org/ns/prov#wasDerivedFrom> <https://doi.org/10.1007/s10344-023-01676-0> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#provenance> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#sig> <http://purl.org/nanopub/x/hasAlgorithm> "RSA" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#sig> <http://purl.org/nanopub/x/hasPublicKey> "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCjDGQCS1S+SRnERDuYDXOugdYUP0efEquHJEEHAbU/uLzBVlga89zqrNPCS7fBE6lArBUWEmT8eLKdMapyqvAzI1J3jUWTMhDJF+XFBkUiuiFfNSc4vJJcmi0yujtnuzXsRIG202jyaP4f5ULoskFwaZOSBZJfiE0dsB3D7DTIAQIDAQAB" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#sig> <http://purl.org/nanopub/x/hasSignature> "BmxFhIUMaljf5MGd6ETv/dTclruWtt0knKiiU9wJPKaq1G3ZfTloNVZB6AckOoKivlQDVr8D8qas4enqbRGhWYLV2se7YMsiMg1lTB09WndovUXp9+5lRIy1s0z1nKF4VqBYEfMNuujtYPyQ8X+cDgqpSjZecrX3iqlBcYlGTD0=" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#sig> <http://purl.org/nanopub/x/hasSignatureTarget> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/dc/terms/created> "2023-09-15T08:54:31.806Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/dc/terms/creator> <https://orcid.org/0000-0002-1267-0234> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/dc/terms/license> <https://creativecommons.org/publicdomain/zero/1.0/> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/nanopub/x/hasNanopubType> <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://purl.org/nanopub/x/introduces> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#association> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <http://www.w3.org/2000/01/rdf-schema#label> "Canis lupus Linnaeus, 1758 (species) - preys on - Bison bison (species)" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <https://w3id.org/np/o/ntemplate/wasCreatedFromProvenanceTemplate> <http://purl.org/np/RAcTpoh5Ra0ssqmcpOgWdaZ_YiPE6demO6cpw-2RvSNs8> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate> <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <https://w3id.org/np/o/ntemplate/wasCreatedFromPubinfoTemplate> <http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> <https://w3id.org/np/o/ntemplate/wasCreatedFromTemplate> <http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0> <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<https://www.checklistbank.org/dataset/2169/taxon/9901> <https://w3id.org/np/o/ntemplate/hasLabelFromApi> "Bison bison (species)" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .
<https://www.checklistbank.org/dataset/9880/taxon/QLXL> <https://w3id.org/np/o/ntemplate/hasLabelFromApi> "Canis lupus Linnaeus, 1758 (species)" <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#pubinfo> .

or via

curl "https://np.petapico.org/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU.trig"

got

@prefix this: <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU> .
@prefix sub: <http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .

sub:Head {
  this: np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo;
    a np:Nanopublication .
}

sub:assertion {
  sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation>;
    rdfs:comment "Wolf (Canis lupus) predation and scavenging of reintroduced bison (Bison bison): a hallmark of ecological restoration to boreal food webs";
    <https://w3id.org/biolink/vocab/object> sub:objtaxon;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002439>;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon;
    <https://w3id.org/kpxl/biodiv/terms/hasSubjectLifeCycleStage> <http://purl.obolibrary.org/obo/UBERON_0018241> .
  
  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/2169/taxon/9901> .
  
  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/QLXL> .
}

sub:provenance {
  sub:assertion prov:wasDerivedFrom <https://doi.org/10.1007/s10344-023-01676-0> .
}

sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCjDGQCS1S+SRnERDuYDXOugdYUP0efEquHJEEHAbU/uLzBVlga89zqrNPCS7fBE6lArBUWEmT8eLKdMapyqvAzI1J3jUWTMhDJF+XFBkUiuiFfNSc4vJJcmi0yujtnuzXsRIG202jyaP4f5ULoskFwaZOSBZJfiE0dsB3D7DTIAQIDAQAB";
    npx:hasSignature "BmxFhIUMaljf5MGd6ETv/dTclruWtt0knKiiU9wJPKaq1G3ZfTloNVZB6AckOoKivlQDVr8D8qas4enqbRGhWYLV2se7YMsiMg1lTB09WndovUXp9+5lRIy1s0z1nKF4VqBYEfMNuujtYPyQ8X+cDgqpSjZecrX3iqlBcYlGTD0=";
    npx:hasSignatureTarget this: .
  
  this: dct:created "2023-09-15T08:54:31.806Z"^^xsd:dateTime;
    dct:creator orcid:0000-0002-1267-0234;
    dct:license <https://creativecommons.org/publicdomain/zero/1.0/>;
    npx:hasNanopubType <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub>;
    npx:introduces sub:association;
    rdfs:label "Canis lupus Linnaeus, 1758 (species) - preys on - Bison bison (species)";
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAcTpoh5Ra0ssqmcpOgWdaZ_YiPE6demO6cpw-2RvSNs8>;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM>,
      <http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90>;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0> .
  
  <https://www.checklistbank.org/dataset/2169/taxon/9901> nt:hasLabelFromApi "Bison bison (species)" .
  
  <https://www.checklistbank.org/dataset/9880/taxon/QLXL> nt:hasLabelFromApi "Canis lupus Linnaeus, 1758 (species)" .
}

jhpoelen · 2023-11-10T00:53:00Z

About the structure of the assertion . . . I was unable to find the definition of some of the biolink terms (e.g., https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation). Is this to be expected? How'd you want species interactions to be modeled in rdf ?

sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation>;
    rdfs:comment "Wolf (Canis lupus) predation and scavenging of reintroduced bison (Bison bison): a hallmark of ecological restoration to boreal food webs";
    <https://w3id.org/biolink/vocab/object> sub:objtaxon;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002439>;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon;
    <https://w3id.org/kpxl/biodiv/terms/hasSubjectLifeCycleStage> <http://purl.obolibrary.org/obo/UBERON_0018241> .
  
  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/2169/taxon/9901> .
  
  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/QLXL> .

jhpoelen · 2023-11-10T00:56:45Z

Also, I noticed that on https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs , there's 2 claims with "source" DOIs. Others appear to be empty. However, in the nanopub assertion there's a neat statement for at least one of the DOI-less ones.

e.g., from http://purl.org/np/RAlfH1ba32D9P9ODv0_pade_yQ8zmPmjPY6CxEXqyj_N8

sub:provenance {
sub:assertion prov:wasGeneratedBy sub:research-activity .
sub:research-activity dct:description https://doi.org/10.3897/zookeys.1181.107496 .
https://doi.org/10.3897/zookeys.1181.107496 a http://purl.org/spar/fabio/ScholarlyWork .
}

but for some reason, https://doi.org/10.3897/zookeys.1181.107496 did not appear in the table version.

Curious to hear your thoughts on keeping the table version integration, or perhaps let GloBI be a little more "semantic". I can see benefits either way. . . curious to hear your thoughts on how to let this integration mature.

tkuhn · 2023-11-10T12:55:40Z

About the structure of the assertion . . . I was unable to find the definition of some of the biolink terms (e.g., https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation). Is this to be expected? How'd you want species interactions to be modeled in rdf ?

sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation>;
    rdfs:comment "Wolf (Canis lupus) predation and scavenging of reintroduced bison (Bison bison): a hallmark of ecological restoration to boreal food webs";
    <https://w3id.org/biolink/vocab/object> sub:objtaxon;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002439>;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon;
    <https://w3id.org/kpxl/biodiv/terms/hasSubjectLifeCycleStage> <http://purl.obolibrary.org/obo/UBERON_0018241> .
  
  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/2169/taxon/9901> .
  
  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/QLXL> .

This seems to be an error at Biolink. This term is defined here: https://biolink.github.io/biolink-model/OrganismTaxonToOrganismTaxonAssociation/

And this page includes a link to the URI you mention above, leading to the same 404 error.

We are using some other terms we had to define in our own namespace, a number of which we still have to properly define. So you might run into some undefined one that are on us.

jhpoelen · 2023-11-24T19:47:35Z

@tkuhn thanks for clarifying the background of the biolink term URIs used.

Note that a first version of the knowledgepixel species interaction claims have been indexed by GloBI

https://www.globalbioticinteractions.org/?accordingTo=globi%3Aglobalbioticinteractions%2Fknowledgepixels&interactionType=ecologicallyRelatedTo

for instance, http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc

@prefix this: <http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc> .
@prefix sub: <http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .

sub:Head {
  this: np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo;
    a np:Nanopublication .
}

sub:assertion {
  sub:association a <https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation>;
    rdfs:comment "The association was established by the amplicon metagenomic analysis of the gut content of the beetles, which revealed DNA of the object taxon.";
    <https://w3id.org/biolink/vocab/object> sub:objtaxon;
    <https://w3id.org/biolink/vocab/predicate> <http://purl.obolibrary.org/obo/RO_0002438>;
    <https://w3id.org/biolink/vocab/subject> sub:subjtaxon .
  
  sub:objtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/6H9MK> .
  
  sub:subjtaxon <https://w3id.org/kpxl/biodiv/terms/hasTaxonName> <https://www.checklistbank.org/dataset/9880/taxon/3K9T3> .
}

sub:provenance {
  sub:assertion prov:wasGeneratedBy sub:research-activity .
  
  sub:research-activity dct:description <https://doi.org/10.3897/zookeys.1181.107496> .
  
  <https://doi.org/10.3897/zookeys.1181.107496> a <http://purl.org/spar/fabio/ScholarlyWork> .
}

sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA";
    npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCIEo4TSFAp5pUug46M+PE3k+rauSFJ/s5jLCNmNL/4XyRjVJ3D8kVq27SCmUY3dY5YvvrpYDZHafJ/cCf3wr3fVcmMTfQJnnAo5t5bPm4Uz1fXRfaoJiUKuSa1P0G2AUBmYUk9WHFDqVUurIXxfLUYKedgnU+R9hQfGbV6SRXWuwIDAQAB";
    npx:hasSignature "JpSYqlrhfbEUA0QN+F99NfbLJPKjpHw+rW2ePjz8Y6ktFVcl18Z0oryo5WL0LAAtZCrquaJcJtzDDuZgsSDbFYyUKsMJJ0kHc1DcD+PPfKi74wy5jk+hCucLW6d+A3yKOJOn2zT1qPMGN2C7Mw7KBSlKYo3KN4e3LLwxEl2HIQo=";
    npx:hasSignatureTarget this: .
  
  this: dct:created "2023-10-02T10:06:51.209Z"^^xsd:dateTime;
    dct:creator orcid:0000-0002-6724-6828;
    dct:license <https://creativecommons.org/licenses/by/4.0/>;
    npx:hasNanopubType <https://w3id.org/kpxl/biodiv/terms/BiodivNanopub>;
    npx:introduces sub:association;
    rdfs:label "Helictopleurus giganteus (Harold, 1869) (species) - trophically interacts with - Eulemur fulvus (É.Geoffroy Saint-Hilaire, 1796) (species)";
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RALfxe37qzq5rEk6tLLcsSeKtKQZ1FcoHZdf2nYVfU66w>;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM>,
      <http://purl.org/np/RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90>;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0> .
  
  <https://www.checklistbank.org/dataset/9880/taxon/3K9T3> nt:hasLabelFromApi "Helictopleurus giganteus (Harold, 1869) (species)" .
  
  <https://www.checklistbank.org/dataset/9880/taxon/6H9MK> nt:hasLabelFromApi "Eulemur fulvus (É.Geoffroy Saint-Hilaire, 1796) (species)" .
}

, was indexed as

Note that name resolving of taxon ids like https://www.checklistbank.org/dataset/9880/taxon/6H9MK is not (yet) supported by GloBI. However, Catalogue of Life taxon ids are (e.g., https://www.catalogueoflife.org/data/taxon/6H9MK).

@tkuhn What was your motivation to point to https://www.checklistbank.org/dataset/9880/taxon/6H9MK ? It appears that the taxon link points to a specific version of a taxonomic checklist instead of pointing to some (aspirational) persistent identifier.

jhpoelen · 2023-11-24T19:49:12Z

@tkuhn Also, I noticed that you are using the relation "trophically interacts with" . I would expect a more directional relationship like "eats". Can you please elaborate?

tkuhn · 2023-11-28T13:06:20Z

@tkuhn What was your motivation to point to https://www.checklistbank.org/dataset/9880/taxon/6H9MK ? It appears that the taxon link points to a specific version of a taxonomic checklist instead of pointing to some (aspirational) persistent identifier.

We chose checklistbank.org because it seemed to be the closest to a universal repository with larger coverage than just catalogueoflife.org, we could get an export that we can use for autocomplete, and we have to deal with just one URI scheme. These URIs seemed as persistent as the catalogueoflife.org ones, but I might be wrong about that. Ultimately we followed the advise by @lyubomirpenev.

tkuhn · 2023-11-28T13:07:00Z

@tkuhn Also, I noticed that you are using the relation "trophically interacts with" . I would expect a more directional relationship like "eats". Can you please elaborate?

I didn't choose it, as it's not my nanopublication :). The given user chose it from a dropdown, which also had "eats" as an option.

tkuhn · 2023-11-28T13:12:12Z

That's the template that the user of the nanopublication above (http://purl.org/np/RA7rvl83o5zWgX7xANozswLg2EQy9EpDDsZ-nACu2OYkc) used to publish it: https://nanodash.petapico.org/publish?template=http://purl.org/np/RAh16oLqLJKo8I8R2CebR1n8Dwv95KL_H-azFfGt2FGW0

jhpoelen · 2023-11-28T13:23:54Z

@tkuhn Also, I noticed that you are using the relation "trophically interacts with" . I would expect a more directional relationship like "eats". Can you please elaborate?

I didn't choose it, as it's not my nanopublication :). The given user chose it from a dropdown, which also had "eats" as an option.

Ha! Perhaps the option should be removed as it doesn't really imply any directionality according to definition:

"ObjectProperty: trophically interacts with
Term IRI: http://purl.obolibrary.org/obo/RO_0002438
Definition: An interaction relationship in which the partners are related via a feeding relationship."

Perhaps this is more of an organizing term, rather than one that should be used directly. Any chance I can convince you (or others) to remove this from the dropdown?

tkuhn · 2023-11-28T13:29:26Z

I tend to agree. We selected the terms based on a hand-curated list by Pensoft, so I am not sure whether they had a good reason to have it on the list.

The full list in nanopub format is here (in the assertion): http://purl.org/np/RAodaWZBY-yDEtl9reYazBfI-YVD5L4zPh8RrVFS0kbEo

This is where the dropdown gets its values from.

Are there any other candidates for removal? @lyubomirpenev, any objections against removing "trophically interacts with"?

lyubomirpenev · 2023-11-28T13:30:09Z

Most important reason: The ChecklistBank one-stop URL is richer in valid names (includes nomenclators!) than the latest version of CoL. Looking into the future, it will be ChecklistBank - e.g. via something like "Catalogue of Life Expanded" - which will provide the most complete list of names with their IDs, unless CoL change their policies to accept all validly published names immediately upon publication (what is unlikely to happen in the foreseeable future). While COL is actually a well-curated taxonomic database, COL Expanded (a new feature of ChecklistBank) should be the place for looking for most complete list of validly published names, including the Catalogue of Life itself.

On 28.11.2023 г. 15:06, Tobias Kuhn wrote: > @tkuhn <https://github.com/tkuhn> What was your motivation to point >

to https://www.checklistbank.org/dataset/9880/taxon/6H9MK > <https://www.checklistbank.org/dataset/9880/taxon/6H9MK> ? It appears > that the taxon link points to a specific version of a taxonomic > checklist instead of pointing to some (aspirational) persistent > identifier. > > We chose checklistbank.org because it seemed to be the closest to a > universal repository with larger coverage than just > catalogueoflife.org, we could get an export that we can use for > autocomplete, and we have to deal with just one URI scheme. These > URIs seemed as persistent as the catalogueoflife.org ones, but I > might be wrong about that. Ultimately we followed the advise by > @lyubomirpenev <https://github.com/lyubomirpenev>. > > — Reply to this email directly, view it on GitHub > <#923 (comment)>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABDFNGKLERIZQBI6LW7WGE3YGXOVPAVCNFSM6AAAAAA5DGTHISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRZHAYDKMJTGY>. > You are receiving this because you were mentioned.Message ID: ***@***.***>

--

Pensoft logo <https://pensoft.net> Prof. Dr. Lyubomir Penev Managing Director Pensoft Publishers <https://pensoft.net> Phone: +359-2-8704281 12 Prof. Georgi Zlatarski Street 1700 Sofia, Bulgaria <https://twitter.com/Pensoft> <https://www.facebook.com/Pensoft/> <https://www.linkedin.com/company/pensoft-publishers/> Blog <https://blog.pensoft.net> valdi names and their

jhpoelen · 2023-11-28T13:30:47Z

@tkuhn What was your motivation to point to https://www.checklistbank.org/dataset/9880/taxon/6H9MK ? It appears that the taxon link points to a specific version of a taxonomic checklist instead of pointing to some (aspirational) persistent identifier.

We chose checklistbank.org because it seemed to be the closest to a universal repository with larger coverage than just catalogueoflife.org, we could get an export that we can use for autocomplete, and we have to deal with just one URI scheme. These URIs seemed as persistent as the catalogueoflife.org ones, but I might be wrong about that. Ultimately we followed the advise by @lyubomirpenev.

Thanks for elaborating. I consider checklist bank more of a registry of checklists, than some kind of authoritative taxonomic resource. So, yes, the coverage is likely to feel more complete, and you might select uncurated checklists. Also, the checklists registered with checklist bank are updated, and they'll get a new URI for each version.

Perhaps a good point of discussion: how to link names to taxonomic resources such that they provide a bridge to the many taxonomic resources associated with that particular name? Right now, it appears as if the user specifically picked the checklist, whereas the actual selection was automated using some algorithm.

lyubomirpenev · 2023-11-28T13:32:37Z

"Trophically interacts with" may have a much wider biological meaning than just "eats". We need to discuss the whole list before starting removing/adding anything from/to there.

On 28.11.2023 г. 15:29, Tobias Kuhn wrote: I tend to agree. We selected the terms based on a hand-curated list by Pensoft, so I am not sure whether they had a good reason to have it on the list. The full list in nanopub format is here (in the assertion): http://purl.org/np/RAodaWZBY-yDEtl9reYazBfI-YVD5L4zPh8RrVFS0kbEo This is where the dropdown gets its values from. Are there any other candidates for removal? @lyubomirpenev <https://github.com/lyubomirpenev>, any objections against removing "trophically interacts with"? — Reply to this email directly, view it on GitHub <#923 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABDFNGLVVQLCTFGCVW6GVJDYGXRMDAVCNFSM6AAAAAA5DGTHISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRZHA2DQMZXGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Pensoft logo <https://pensoft.net> Prof. Dr. Lyubomir Penev Managing Director Pensoft Publishers <https://pensoft.net> Phone: +359-2-8704281 12 Prof. Georgi Zlatarski Street 1700 Sofia, Bulgaria <https://twitter.com/Pensoft> <https://www.facebook.com/Pensoft/> <https://www.linkedin.com/company/pensoft-publishers/> Blog <https://blog.pensoft.net>

jhpoelen · 2023-11-28T13:44:29Z

"Trophically interacts with" may have a much wider biological meaning
than just "eats". We need to discuss the whole list before starting
removing/adding anything from/to there.

I agree that a discussion on how to represent the terms would be in order before handpicking them.

My main concern is that folks may be picking the more convenient option for some reason (closest in drop-down, more familiar language) instead of picking the one that best aligned with what an author may have expressed in the annotated work. Perhaps some example for usage may help folks to decide what to choose? (e.g., guidelines - be as specific as you can be, using directional interaction types when suitable).

jhpoelen · 2023-11-28T13:49:38Z

@lyubomirpenev thanks for elaborating

The ChecklistBank one-stop URL is richer in valid
names (includes nomenclators!) than the latest version of CoL.

Yes, and I assume that there's many possible matches within checklist bank for a single name. I wonder how to make sure that a single name URL is not interpreted as "the" single name URL.

lyubomirpenev · 2023-11-28T17:15:03Z

This can be ensured by versioning history which, as far as I know, is maintained by CLB. Otherwise, the basic idea to have "stable CLB PIDs" fir names that are or will be linked to the COL canonical names PIDs is the feature we want to develop in BiCIKL+ (if successful).There is a definite need in such service and CLB know about that.At the very end, it is better to have an ID for a name based on an ID of the taxon name usage in a particular ID, than not to have any ID nor a reference link for a name.На 28.11.2023 г. 15:49 ч. Jorrit Poelen ***@***.***> написа: @lyubomirpenev thanks for elaborating The ChecklistBank one-stop URL is richer in valid names (includes nomenclators!) than the latest version of CoL. Yes, and I assume that there's many possible matches within checklist bank for a single name. I wonder how to make sure that a single name URL is not interpreted as "the" single name URL. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

…ted to #923

tkuhn · 2023-12-05T09:23:38Z

Here some responses by Andrey Frolov, who created the nanopublications we discussed above ("trophically interacts with") and who gave me permission to paste his explanation for the choice here:

As for "trophically interacts with" vs "eats" - I selected the most appropriate, I thought, because beetles do not eat lemurs but eat their "products". It may be a bit vague term but I think it was best of the possible choices.

I re-checked the options available during new nanopub creation. Perhaps "acquires nutrients from" is better than more general "trophically interacts with", but is still somewhat misleading in my view because, like "eats", it implies that the subject acquires something for the object itself and not from a "product" of the object. Just in case, we are studying dung beetles that feed on droppings of mammals.

jhpoelen · 2023-12-05T13:28:22Z

@tkuhn thanks for sharing Andrey Frolov's response.

As I was reading it, I was wondering whether it would have helped to use "body part" as "feces" . Or perhaps be more descriptive like: beetle eats the feces produced by a lemur, where feces is an abiotic thing, and "producing" would be some other verb/predicate.

Great how these nanopublications help to facilitate these discussions!

…oticinteractions/globalbioticinteractions#923

jhpoelen · 2024-05-28T15:54:40Z

species interaction claims on BDJ via KnowledgePixels are actively indexed by GloBI.

See e.g.,

https://www.globalbioticinteractions.org/?accordingTo=globi%3Aglobalbioticinteractions%2Fknowledgepixels&interactionType=ecologicallyRelatedTo

jhpoelen pushed a commit to globalbioticinteractions/knowledgepixels that referenced this issue Sep 27, 2023

add first attempt to index @tkuhn nanopubs; see related globalbiotici…

56b09e4

…nteractions/globalbioticinteractions#923

jhpoelen pushed a commit to globalbioticinteractions/elton that referenced this issue Sep 29, 2023

add testcase to help reproduce globalbioticinteractions/globalbiotici…

86f03e7

…nteractions#923 (comment) ; fyi @tkuhn

jhpoelen pushed a commit that referenced this issue Sep 29, 2023

reproduce error in #923 (comment); fyi @tkuhn

f215052

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jhpoelen pushed a commit that referenced this issue Nov 3, 2023

add Accept Header to make grlc happy. Related to #923 (comment) fyi @…

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…tkuhn

jhpoelen changed the title ~~index nanopubs on BDJ~~ index nanopubs with species interaction claims on BDJ Nov 10, 2023

jhpoelen changed the title ~~index nanopubs with species interaction claims on BDJ~~ index nanopubs with species interaction claims on BDJ via KnowledgePixels Nov 10, 2023

jhpoelen added the needs review label Nov 24, 2023

jhpoelen mentioned this issue Nov 28, 2023

export annotation on a specific record to web annotation format globalbioticinteractions/carvalheiro2023#4

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jhpoelen pushed a commit that referenced this issue Nov 28, 2023

add support for TROPHICALLY_INTERACTS_WITH related to #923

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updated test after adding support for TROPHICALLY_INTERACTS_WITH rela…

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…ted to #923

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take a elton nanopub and translate into web annotation format globalbioticinteractions/carvalheiro2023#6

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include taxonlabels for ease of human readability related to globalbi…

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…oticinteractions/globalbioticinteractions#923

jhpoelen mentioned this issue Jan 4, 2024

include taxonlabels for ease of human readability related to https://… knowledgepixels/bdj-nanopub-api#1

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jhpoelen closed this as completed May 28, 2024

index nanopubs with species interaction claims on BDJ via KnowledgePixels #923

index nanopubs with species interaction claims on BDJ via KnowledgePixels #923

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