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A formalization of one of the main claims of “OpenBiodiv: A knowledge graph for literature-extracted linked open data in biodiversity science” by Penev et al. 20191

Issue title: Semantic Publishing with Formalization Papers

Guest editors: Cristina-Iulia Bucur and Tobias Kuhn

Article type: Formalization Paper

Authors: Dimitrova, Mariya; *

Affiliations: Bulgarian Academy of Sciences, Bulgaria and Pensoft Publishers, Bulgaria

Correspondence: [*] Corresponding author. E-mail: m.dimitrova@pensoft.net.

Note: [1] As RDF/nanopublication: http://purl.org/np/RAMgThXW6xx8QiPmW9VhVuxWCN2ZWe-pmxDcFfdx_A7z0

Keywords: release of OpenBiodiv knowledge graph, triple in OpenBiodiv knowledge graph, semantic triple extracted from biodiversity literature

DOI: 10.3233/DS-210045

Journal: Data Science, vol. 5, no. 1, pp. 43-47, 2022

Received 7 July 2021
|
Accepted 3 December 2021
|
Published: 22 March 2022
Get PDF open access

Abstract

Penev et al. claimed in previous work that triples in the OpenBiodiv knowledge graph releases are generally semantic triples extracted from biodiversity literature. We present here a formalization of that claim, stating that all things of class “triple in OpenBiodiv knowledge graph” that are in the context of a thing of class “release of OpenBiodiv knowledge graph” generally have a relation of type “is same as” to a thing of class “semantic triple extracted from biodiversity literature” in the same context.

1.Introduction

Penev et al. [2] state that “OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone.”. We present here a formalization of the main scientific claim from this quote by using a semantic template called the super-pattern [1].

2.Formalization

Our formalization looks as follows:

CONTEXT-CLASS (“in the context of all…”):release of OpenBiodiv knowledge graph
SUBJECT-CLASS (“things of type…”):triple in OpenBiodiv knowledge graph
QUALIFIER:generally
RELATION-TYPE (“have a relation of type…”):is same as
OBJECT-CLASS (“to things of type…”):semantic triple extracted from biodiversity literature

In the context class we use a new minted class “release of OpenBiodiv knowledge graph” that is a subclass of “software release” (Q20631656) from Wikidata and has a related class a new minted class “OpenBiodiv knowledge graph” that is a subclass of the “knowledge graph” (Q33002955) class from Wikidata. In the subject class, we use a new minted class “triple in OpenBiodiv knowledge graph” that is related to a new minted class “OpenBiodiv knowledge graph” that is a subclass of the “knowledge graph” (Q33002955) class from Wikidata. In the object class we minted a new class “semantic triple extracted from biodiversity literature” that is related to a new minted class “OpenBiodiv knowledge graph” that is a subclass of the “knowledge graph” (Q33002955) class from Wikidata.

3.RDF code

This is our formalization as a nanopublication in TriG format:

@prefix this: <http://purl.org/np/RAMgThXW6xx8QiPmW9VhVuxWCN2ZWe-pmxDcFfdx_A7z0> .
@prefix sub: <http://purl.org/np/RAMgThXW6xx8QiPmW9VhVuxWCN2ZWe-pmxDcFfdx_A7z0#> .
@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#> .
@prefix sp: <https://w3id.org/linkflows/superpattern/terms/> .

sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:spi a sp:SuperPatternInstance ;
    rdfs:label "Triples in the OpenBiodiv knowledge graph releases are generally semantic triples extracted from biodiversity
literature." ;
    sp:hasContextClass <http://purl.org/np/RAlm6vh2zpFLg189qrDYPtppkL790Pqaw-q2KUhyfJtRY#release-of-openbiodiv-knowledge-
graph> ;
    sp:hasSubjectClass <http://purl.org/np/RAaEkIiJLmBJP5kK3JdYjseCRqwutYbdnI8Q3VbzrK9VA#triple-in-openbiodiv-knowledge-
graph> ;
    sp:hasQualifier sp:generallyQualifier ;
    sp:hasRelation sp:isSameAs ;
    sp:hasObjectClass <http://purl.org/np/RAEpHUXRKtaLE3Z24sgIUdaxwTBsK2bjshyq9yF00145Y#semantic-triples-extracted-from-
biodiversity-literature> .
}
sub:provenance {
  sub:activity a sp:FormalizationActivity ;
    prov:used sub:quote , <https://doi.org/10.3390/publications7020038> ;
    prov:wasAssociatedWith orcid:0000-0002-8083-6048 .
  sub:assertion prov:wasGeneratedBy sub:activity .
  sub:quote prov:value "OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and
many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted
to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version
of the Global Biodiversity Information Facility (GBIF) taxonomic backbone." ;
    prov:wasQuotedFrom <https://doi.org/10.3390/publications7020038> .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwi1YMnpV5z/0oMXyFYDKS5cirQQWTMZ/jbglmVY1gl3YAgrkqsQUmgaxA/ho+VV8jsfREIL8PT2czbmCjGjMJ
oNaKVqJq1GoIUV9+Kj9yXxNySyDAOTDsIM0zdj1BEu5uNbtfzwQPGuhVpgLR05Uk/meCyYLPs3BxC5zRbtulmwIDAQAB" ;
    npx:hasSignature
"ZbscFpNaJ3Wi/kWcKUWM3P5FbINnIPh3Z/BHMuCI95sAZjbD6XQD4AVUf7XUfFcMZtK8QKRE6S88zdLayXPklZC2x2GWcrh0j7Rk5UisHVcyZrukL0jH0D7oxXw2
xi+W1FhX+6X8cgilEcums1MTLZ9bx3BdA1Goii6pR32gOLQ=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-30T22:13:32.063+02:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-8083-6048 ;
    npx:introduces sub:spi ;
    npx:supersedes <http://purl.org/np/RAN_chNfWR9hbEkfjwOfMpq1piwOgAj6q2sJ-qbDzaLOk> ;
    <https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAWcrMY8mnsI26BfokKid75MO1c2uVenyW9tmxj0VhbnY> ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAE1wniOy0yO39PlK9QkQ-wqbC3q-R2nXraP5huu8W39k> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RA2vCBXZf-icEcVRGhulJXugTGxpsV5yVr9yqCI1bQh4A> ,
<http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAv68imZrEjfcp2rnEg1hzoBqEVc0cQMtp9_1Za0BxNM4> .
}

The following nanopublications introduce the newly minted classes in TriG format.

This is the class definition of “release of OpenBiodiv knowledge graph”:

@prefix this: <http://purl.org/np/RAlm6vh2zpFLg189qrDYPtppkL790Pqaw-q2KUhyfJtRY> .
@prefix sub: <http://purl.org/np/RAlm6vh2zpFLg189qrDYPtppkL790Pqaw-q2KUhyfJtRY#> .
@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#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:release-of-openbiodiv-knowledge-graph a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "A release of the OpenBiodiv knowledge graph" ;
    rdfs:subClassOf <http://www.wikidata.org/entity/Q20631656> ;
    skos:definition "A release of the OpenBiodiv knowledge graph stored in a GraphDB repository at http://graph.openbiodiv.
net/" ;
    skos:relatedMatch <http://purl.org/np/RAY2Gg01ffDVLprAakuMqpizAjksasRtTal_UsCf94LL8#openbiodiv-knowledge-graph> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-8083-6048 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwi1YMnpV5z/0oMXyFYDKS5cirQQWTMZ/jbglmVY1gl3YAgrkqsQUmgaxA/ho+VV8jsfREIL8PT2czbmCjGjMJ
oNaKVqJq1GoIUV9+Kj9yXxNySyDAOTDsIM0zdj1BEu5uNbtfzwQPGuhVpgLR05Uk/meCyYLPs3BxC5zRbtulmwIDAQAB" ;
    npx:hasSignature
"FXDBQ2xJ6NWoC7ai62Yd02KL1I45X1XQxAN1skRMXtENVvO0ZdzjKOjU8TBOyw23h1prP/Ei/k+BT2JgOVHS+LyJXoW0ncHMg9a9AFrhB/BX+S6SMLVCEh0h8uzD
7GbnBv6Vet2ajQ7nWCSb4ZkTJa0iByrFU/bpQMBZ4JKvkRs=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-30T22:05:24.772+02:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-8083-6048 ;
    npx:introduces sub:release-of-openbiodiv-knowledge-graph ;
    npx:supersedes <http://purl.org/np/RAySzPQKOPqboKwpMIeTtYhCwmLZTdlmKhiMM9W_fmZKw> ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

This is the class definition of “triple in OpenBiodiv knowledge graph”:

@prefix this: <http://purl.org/np/RAaEkIiJLmBJP5kK3JdYjseCRqwutYbdnI8Q3VbzrK9VA> .
@prefix sub: <http://purl.org/np/RAaEkIiJLmBJP5kK3JdYjseCRqwutYbdnI8Q3VbzrK9VA#> .
@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#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:triple-in-openbiodiv-knowledge-graph a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "Triple in OpenBiodiv knowledge graph" ;
    skos:definition "A semantic triple in the OpenBiodiv knowledge graph" ;
    skos:relatedMatch <http://purl.org/np/RAY2Gg01ffDVLprAakuMqpizAjksasRtTal_UsCf94LL8#openbiodiv-knowledge-graph> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-8083-6048 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwi1YMnpV5z/0oMXyFYDKS5cirQQWTMZ/jbglmVY1gl3YAgrkqsQUmgaxA/ho+VV8jsfREIL8PT2czbmCjGjMJ
oNaKVqJq1GoIUV9+Kj9yXxNySyDAOTDsIM0zdj1BEu5uNbtfzwQPGuhVpgLR05Uk/meCyYLPs3BxC5zRbtulmwIDAQAB" ;
    npx:hasSignature
"dPpPA1yEeyfIBRllzfX4pmiOoCUzGAxPLEf8+1/1CWBAecvBCtqsS+rUAWUnHEqHytgrvWlxZhEmw7oC3ilPPIl3Pkb8NwiJ1BcRgLOPbe2R5+1ws75TDzmaZKjU
oHoMbB4oBIfT78o4YcULeUOiZww19rVWvddCv/JlXc2nSk8=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-30T22:09:26.986+02:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-8083-6048 ;
    npx:introduces sub:triple-in-openbiodiv-knowledge-graph ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

This is the class definition of “semantic triple extracted from biodiversity literature”:

@prefix this: <http://purl.org/np/RAEpHUXRKtaLE3Z24sgIUdaxwTBsK2bjshyq9yF00145Y> .
@prefix sub: <http://purl.org/np/RAEpHUXRKtaLE3Z24sgIUdaxwTBsK2bjshyq9yF00145Y#> .
@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#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:semantic-triples-extracted-from-biodiversity-literature a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "semantic triple extracted from biodiversity literature" ;
    rdfs:subClassOf <http://www.wikidata.org/entity/Q3539534> ;
    skos:definition "semantic triple generated after information was extracted from biodiversity literature" ;
    skos:relatedMatch <http://purl.org/np/RAMZHs5RfS70gZEtxxJjQtvsXZ03BBINhDPowhiqQ5WnU#semantic-triples-generated-from-XML-
files> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-8083-6048 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwi1YMnpV5z/0oMXyFYDKS5cirQQWTMZ/jbglmVY1gl3YAgrkqsQUmgaxA/ho+VV8jsfREIL8PT2czbmCjGjMJ
oNaKVqJq1GoIUV9+Kj9yXxNySyDAOTDsIM0zdj1BEu5uNbtfzwQPGuhVpgLR05Uk/meCyYLPs3BxC5zRbtulmwIDAQAB" ;
    npx:hasSignature
"MAKvDuDjhzerLDcmY46TxIDqqtyyUtkGAfkKhR107rtMwn7BwyIRLijiyIGjrjzQDeOkMQhPw0N8TlDXuMfp1N6C0QuSY6nbWnvMDM6tFVgxD3n7AHjPutj5N9Ru
mjNlPzYffkzGyIA9BryrgzjAc6dEBn3VTJI1phJi7toCGjk=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-07-07T10:58:43.199+03:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-8083-6048 ;
    npx:introduces sub:semantic-triples-extracted-from-biodiversity-literature ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

This is the class definition of “OpenBiodiv knowledge graph”:

@prefix this: <http://purl.org/np/RAY2Gg01ffDVLprAakuMqpizAjksasRtTal_UsCf94LL8> .
@prefix sub: <http://purl.org/np/RAY2Gg01ffDVLprAakuMqpizAjksasRtTal_UsCf94LL8#> .
@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#> .
@prefx skos: <http://www.w3.org/2004/02/skos/core#> .

sub:Head {
  this: np:hasAssertion sub:assertion ;
    np:hasProvenance sub:provenance ;
    np:hasPublicationInfo sub:pubinfo ;
    a np:Nanopublication .
}
sub:assertion {
  sub:openbiodiv-knowledge-graph a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "OpenBiodiv knowledge graph" ;
    rdfs:subClassOf <http://www.wikidata.org/entity/Q33002955> ;
    skos:definition "a knowledge graph containing statements extracted from biodiversity literature" .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-8083-6048 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwi1YMnpV5z/0oMXyFYDKS5cirQQWTMZ/jbglmVY1gl3YAgrkqsQUmgaxA/ho+VV8jsfREIL8PT2czbmCjGjMJ
oNaKVqJq1GoIUV9+Kj9yXxNySyDAOTDsIM0zdj1BEu5uNbtfzwQPGuhVpgLR05Uk/meCyYLPs3BxC5zRbtulmwIDAQAB" ;
    npx:hasSignature
"WDSCKwvQnBIPTel8btfovXycebML+Pg+GVVREG15t1f5BTDrldaJGO8FN3K7rsCHp3Sel25pJyV3aySvg/lcEUFMHi46Xtxtyu1isZF7FQ0BVHM7zx+nacgxm4UW
8lQMG0e9l9OUypkyQtVHphyXzgcE8L6qK+PonrSFp5twfy0=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-07-07T09:30:53.628+03:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-8083-6048 ;
    npx:introduces sub:openbiodiv-knowledge-graph ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

Funding

This research received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement IGNITE (No. 764840).

References

[1] 

C.I. Bucur, T. Kuhn, D. Ceolin and J. van Ossenbruggen, Expressing high-level scientific claims with formal semantics, Proceedings of the 11th Knowledge Capture Conference 2021. doi:10.1145/3460210.3493561.

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L. Penev, M. Dimitrova, V. Senderov, G. Zhelezov, T. Georgiev, P. Stoev, Simov and K. OpenBiodiv, A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science, Vol. 7: , Publications, (2019) , p. 38. doi:10.3390/publications7020038.

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