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A formalization of one of the main claims of “The cancer glycocalyx mechanically primes integrin-mediated growth and survival” by Paszek et al. 20141

Issue title: Semantic Publishing with Formalization Papers

Guest editors: Cristina-Iulia Bucur and Tobias Kuhn

Article type: Formalization Paper

Authors: Bainer, Russell; *

Affiliations: Maze Therapeutics, USA

Correspondence: [*] Corresponding author. E-mail: [email protected].

Note: [1] As RDF/nanopublication: http://purl.org/np/RAoo8EvTgfkxJw5SgZXbJvRl5nQG7ygeGaHp8Zud1U4Zw

Keywords: ecm bound cancer cell, glycocalyx bulk, integrin clustering

DOI: 10.3233/DS-210050

Journal: Data Science, vol. 5, no. 1, pp. 65-69, 2022

Received 18 June 2021
|
Accepted 29 November 2021
|
Published: 22 March 2022
Get PDF open access

Abstract

Paszek et al. claimed in previous work that glycocalyx bulk mechanically drives integrin clustering in cancer cells engaged with the extracellular matrix. We present here a formalization of that claim, stating that all things of class “glycocalyx bulk” that are in the context of a thing of class “ecm bound cancer cell” generally have a relation of type “increases” to a thing of class “integrin clustering” in the same context.

1.Introduction

Paszek et al. [2] state that “Expression of large tumour-associated glycoproteins in non-transformed mammary cells promoted focal adhesion assembly and facilitated integrin-dependent growth factor signalling to support cell growth and survival.”. 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…”):ecm bound cancer cell
SUBJECT-CLASS (“things of type…”):glycocalyx bulk
QUALIFIER:generally
RELATION-TYPE (“have a relation of type…”):increases
OBJECT-CLASS (“to things of type…”):integrin clustering

In the context class we use a new minted class “ecm bound cancer cell” that is a subclass of “cancer cell” (Q4118072) from Wikidata and is related to the class “extracellular matrix” (Q193825) from Wikidata. In the subject class, we use a new minted class “glycocalyx bulk” that is related to the class “glycocalyx” (Q898356) from Wikidata. In the object class we minted a new class “integrin clustering” that is a subclass of “integrin binding” (Q14633861) from Wikidata and is related to the class “focal adhesion” (Q904514) from Wikidata.

3.RDF code

This is our formalization as a nanopublication in TriG format:

@prefix this: <http://purl.org/np/RAoo8EvTgfkxJw5SgZXbJvRl5nQG7ygeGaHp8Zud1U4Zw> .
@prefix sub: <http://purl.org/np/RAoo8EvTgfkxJw5SgZXbJvRl5nQG7ygeGaHp8Zud1U4Zw#> .
@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 "Glycocalyx bulk mechanically drives integrin clustering in cancer cells engaged with the extracellular matrix" ;
    sp:hasContextClass <http://purl.org/np/RAaOAF90U6YxAvnchfj0dRtT5HRz320Pz202aGap-VfuI#ecm-bound-cancer-cell> ;
    sp:hasSubjectClass <http://purl.org/np/RA-jkb7qPNTSOe_EXltW_rlQWQ9x3_Y1KOzW6J_bbPz4U#glycocalyx-bulk> ;
    sp:hasQualifier <https://w3id.org/linkflows/superpattern/terms/generallyQualifier> ;
    sp:hasRelation <https://w3id.org/linkflows/superpattern/terms/increases> ;
    sp:hasObjectClass <http://purl.org/np/RAFH8AVn-wnTcSGxvPZ1Uiy_AtOhINlynnAxxiCdcTVWU#integrin-clustering> .
}
sub:provenance {
  sub:activity a sp:FormalizationActivity ;
    prov:used sub:quote , <https://www.nature.com/articles/nature13535> ;
    prov:wasAssociatedWith orcid:0000-0002-0830-7029 .
  sub:assertion prov:wasGeneratedBy sub:activity .
  sub:quote prov:value "Expression of large tumour-associated glycoproteins in non-transformed mammary cells promoted focal
adhesion assembly and facilitated integrin-dependent growth factor signalling to support cell growth and survival." ;
    prov:wasQuotedFrom <https://www.nature.com/articles/nature13535> .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCluZ2msgo7OqPkyRoZMluzpaLX8KRHyDs3J/cZwm6+Vq/CKVIGsGaT7/XH435cE9J8dwCgQ/Jssjlj6oqX+nSI9x
XBtMH9ZeyGHFBzK1cUBy/rRSez4EnwbS1sKMBSc4MBCXQ9R3jZ3GpsN0GmIrS1ukKkUBQrREBYpb4w5MbGywIDAQAB" ;
    npx:hasSignature
"Mc6yNlLGIu3AnhZEmrajdDXbYISe2imFa8OBDfBIWbQvJlOdxKaohx+dR9jwbzecksZ+bMNvtojD/ftMxBeLu3126L1DmW0kxIWoTvfi+RRhgeaXTkRT/RV7EB
mcuEfzEU6Lk3YkK/v4dOiCP24mei1YLdsNRLK4n44AvOr54lE=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-26T17:14:38.341-07:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-0830-7029 ;
    npx:introduces sub:spi ;
    npx:supersedes <http://purl.org/np/RAh1GOK4_HhqeUeJhIyV_DDCFFTY9jeeiKWgbSzooWEi4> ;
    <https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RASZZ5T1Ca5gpCMPubKoypR_0WcSUkHiMaADu9o1BS1Xs> ;
    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 “ecm bound cancer cell”:

@prefix this: <http://purl.org/np/RAaOAF90U6YxAvnchfj0dRtT5HRz320Pz202aGap-VfuI> .
@prefix sub: <http://purl.org/np/RAaOAF90U6YxAvnchfj0dRtT5HRz320Pz202aGap-VfuI#> .
@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:ecm-bound-cancer-cell a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "cancer cell engaged in extracellular matrix" ;
    rdfs:subClassOf <http://www.wikidata.org/entity/Q4118072> ;
    skos:definition "cancer cell engaged in extracellular matrix" ;
    skos:relatedMatch <http://www.wikidata.org/entity/Q193825> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-0830-7029 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCluZ2msgo7OqPkyRoZMluzpaLX8KRHyDs3J/cZwm6+Vq/CKVIGsGaT7/XH435cE9J8dwCgQ/Jssjlj6oqX+nSI9x
XBtMH9ZeyGHFBzK1cUBy/rRSez4EnwbS1sKMBSc4MBCXQ9R3jZ3GpsN0GmIrS1ukKkUBQrREBYpb4w5MbGywIDAQAB" ;
    npx:hasSignature
"J5J3Blgx/OmReiNFC8+4TzqHm34UUmKcQKRhq7SVPq5H0rLE0fqyX4RfZfA0oQg5dfD7vnbVttaGsUQZs1Iw1dU4r/CYko2IXUQiptdcY28cR76t/4coiBcFCZpqy
3GPTKwIj7uR/aJIUj4UDzA6LCmsWju0hT1bp5NDmNhT+8E=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-12T09:21:35.816-08:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-0830-7029 ;
    npx:introduces sub:ecm-bound-cancer-cell ;
    npx:supersedes <http://purl.org/np/RAXecDWH8gZVp7FZRP1m_Fg6EXH_uoZGhKN9blfN9lrfI> ;
    <https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RAXecDWH8gZVp7FZRP1m_Fg6EXH_uoZGhKN9blfN9lrfI> ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAOGu9Lh0BD4tbIRB9RG6RGRA_ObDh75NTbIqaWgxxs8M> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

This is the class definition of “glycocalyx bulk”:

@prefix this: <http://purl.org/np/RA-jkb7qPNTSOe_EXltW_rlQWQ9x3_Y1KOzW6J_bbPz4U> .
@prefix sub: <http://purl.org/np/RA-jkb7qPNTSOe_EXltW_rlQWQ9x3_Y1KOzW6J_bbPz4U#> .
@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:glycocalyx-bulk a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "glycocalyx bulk" ;
    skos:definition "Relating to size, density, or bulk of the glycocalyx" ;
    skos:relatedMatch <http://www.wikidata.org/entity/Q898356> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-0830-7029 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCluZ2msgo7OqPkyRoZMluzpaLX8KRHyDs3J/cZwm6+Vq/CKVIGsGaT7/XH435cE9J8dwCgQ/Jssjlj6oqX+nSI9x
XBtMH9ZeyGHFBzK1cUBy/rRSez4EnwbS1sKMBSc4MBCXQ9R3jZ3GpsN0GmIrS1ukKkUBQrREBYpb4w5MbGywIDAQAB" ;
    npx:hasSignature
"WlbAvo5qWbVaY31i3E/uayLdSkt0IFbe2m+P7z0CEaoghb+sTAehmDjw9pmd2bzPQFblGdIwBr5yhGHXGorM4v3bkV2nIiRecOwhvtu9hM2pIUtS8QwD6kggHsO1Wxz
T4Wqs3GmS63PgN3cxZjEs0BuTWUhiXbd2V6gkLUPvaK8=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-12T09:27:02.246-08:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-0830-7029 ;
    npx:introduces sub:glycocalyx-bulk ;
    npx:supersedes <http://purl.org/np/RACS5sSm45MGbuJrztnPrpdu1AuLiKxDni-6JcKzN5ZtM> ;
    <https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RACS5sSm45MGbuJrztnPrpdu1AuLiKxDni-6JcKzN5ZtM> ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAOGu9Lh0BD4tbIRB9RG6RGRA_ObDh75NTbIqaWgxxs8M> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

This is the class definition of “integrin clustering”:

@prefix this: <http://purl.org/np/RAFH8AVn-wnTcSGxvPZ1Uiy_AtOhINlynnAxxiCdcTVWU> .
@prefix sub: <http://purl.org/np/RAFH8AVn-wnTcSGxvPZ1Uiy_AtOhINlynnAxxiCdcTVWU#> .
@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:integrin-clustering a <http://www.w3.org/2002/07/owl#Class> ;
    rdfs:label "integrin clustering" ;
    rdfs:subClassOf <http://www.wikidata.org/entity/Q14633861> ;
    skos:definition "clustering of integrin proteins at a focal adhesion" ;
    skos:relatedMatch <http://www.wikidata.org/entity/Q904514> .
}
sub:provenance {
  sub:assertion prov:wasAttributedTo orcid:0000-0002-0830-7029 .
}
sub:pubinfo {
  sub:sig npx:hasAlgorithm "RSA" ;
    npx:hasPublicKey
"MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCluZ2msgo7OqPkyRoZMluzpaLX8KRHyDs3J/cZwm6+Vq/CKVIGsGaT7/XH435cE9J8dwCgQ/Jssjlj6oqX+nSI9x
XBtMH9ZeyGHFBzK1cUBy/rRSez4EnwbS1sKMBSc4MBCXQ9R3jZ3GpsN0GmIrS1ukKkUBQrREBYpb4w5MbGywIDAQAB" ;
    npx:hasSignature
"Bw052zD4Sd8+EkXb26m8oz03UEYZVfzKsvkEbf3j/zJeQJ/2PsYF94kN6QBs0mKoSeHJJQxOMOer6WCcTbYmltvLgG2zQYEFC3wkhRMTx5eEVjEMAXx4S57/Ur2a5y
h+HzyqELJ1jG+2JIUQdHKO8F0F0VUqB2tyEf/ZhjMFz10=" ;
    npx:hasSignatureTarget this: .
  this: dct:created "2021-11-12T09:17:34.478-08:00"^^xsd:dateTime ;
    dct:creator orcid:0000-0002-0830-7029 ;
    npx:introduces sub:integrin-clustering ;
    npx:supersedes <http://purl.org/np/RA9UaQM3wVa9xRAmL9CWEXyhDbcgvHlPoGTw4pnKaHYL8> ;
    <https://w3id.org/linkflows/reviews/isUpdateOf> <http://purl.org/np/RA9UaQM3wVa9xRAmL9CWEXyhDbcgvHlPoGTw4pnKaHYL8> ;
    nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
    nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ,
<http://purl.org/np/RAOGu9Lh0BD4tbIRB9RG6RGRA_ObDh75NTbIqaWgxxs8M> ,
<http://purl.org/np/RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI> ;
    nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}

References

[1] 

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

[2] 

M. Paszek, C. DuFort, O. Rossier et al., The cancer glycocalyx mechanically primes integrin-mediated growth and survival, Nature 511: ((2014) ), 319–325. doi:10.1038/nature13535.

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