FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-12

AUTHORS

Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock

ABSTRACT

BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. DESCRIPTION: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. CONCLUSIONS: Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores. More... »

PAGES

39

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13326-016-0067-z

DOI

http://dx.doi.org/10.1186/s13326-016-0067-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010925225

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27296299


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Biological Ontologies", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Protein", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fuzzy Logic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Annotation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleotides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reference Books", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Semantics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Swiss Institute of Bioinformatics", 
          "id": "https://www.grid.ac/institutes/grid.419765.8", 
          "name": [
            "Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel, Servet, 1211, Geneva 4, Switzerland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bolleman", 
        "givenName": "Jerven T.", 
        "id": "sg:person.01300247434.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300247434.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Berkeley National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.184769.5", 
          "name": [
            "Genomics Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mungall", 
        "givenName": "Christopher J.", 
        "id": "sg:person.011151027407.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011151027407.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Parco Tecnologico Padano", 
          "id": "https://www.grid.ac/institutes/grid.425375.2", 
          "name": [
            "CeRSA, Parco Tecnologico Padano, 26900, Lodi, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Strozzi", 
        "givenName": "Francesco", 
        "id": "sg:person.01320675003.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320675003.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "CODAMONO, 5-121 Marion Street, M6R 1E6, Toronto, Ontario, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Baran", 
        "givenName": "Joachim", 
        "id": "sg:person.0660120074.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0660120074.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, 94305-5479, Stanford, CA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dumontier", 
        "givenName": "Michel", 
        "id": "sg:person.01324655201.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01324655201.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Istituto Nazionale Genetica Molecolare", 
          "id": "https://www.grid.ac/institutes/grid.428717.f", 
          "name": [
            "Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bonnal", 
        "givenName": "Raoul J. P.", 
        "id": "sg:person.012665544347.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012665544347.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, Berkeley", 
          "id": "https://www.grid.ac/institutes/grid.47840.3f", 
          "name": [
            "University of California, Berkeley, Berkeley, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Buels", 
        "givenName": "Robert", 
        "id": "sg:person.0712511300.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712511300.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Computer Science, SY23 3DB, Aberystwyth, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hoehndorf", 
        "givenName": "Robert", 
        "id": "sg:person.01300743466.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300743466.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Institute of Genetics", 
          "id": "https://www.grid.ac/institutes/grid.288127.6", 
          "name": [
            "Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-08540, Shizuoka, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fujisawa", 
        "givenName": "Takatomo", 
        "id": "sg:person.0775625561.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775625561.49"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Research Organization of Information and Systems", 
          "id": "https://www.grid.ac/institutes/grid.418987.b", 
          "name": [
            "Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Katayama", 
        "givenName": "Toshiaki", 
        "id": "sg:person.01237652002.94", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01237652002.94"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "James Hutton Institute", 
          "id": "https://www.grid.ac/institutes/grid.43641.34", 
          "name": [
            "The James Hutton Institute, DD2 5DA, Dundee, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Cock", 
        "givenName": "Peter J. A.", 
        "id": "sg:person.01150006507.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150006507.62"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/nar/gks1068", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000076796"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl647", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000310618"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/glycob/cwj049", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002645985"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/glycob/cwj049", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002645985"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2041-1480-2-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004132434", 
          "https://doi.org/10.1186/2041-1480-2-6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks1152", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004169169"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkt1128", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007987025"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2041-1480-2-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008246254", 
          "https://doi.org/10.1186/2041-1480-2-4"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2041-1480-1-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008414706", 
          "https://doi.org/10.1186/2041-1480-1-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.7717/peerj.933", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009614731"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.094607.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010225667"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp163", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011232850"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2041-1480-4-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016886003", 
          "https://doi.org/10.1186/2041-1480-4-6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks1175", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024766283"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2010-11-8-r88", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025532561", 
          "https://doi.org/10.1186/gb-2010-11-8-r88"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1042/bj0450563", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026481020"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1042/bj0450563", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026481020"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2005-6-5-r44", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026484271", 
          "https://doi.org/10.1186/gb-2005-6-5-r44"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.361602", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028020859"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bts494", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030116406"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btq475", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033174360"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks1195", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035881992"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkq1014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037469099"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2041-1480-5-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046582343", 
          "https://doi.org/10.1186/2041-1480-5-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkq733", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048436860"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm189", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051261157"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ci100150d", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055402421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ci100150d", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055402421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/omi.2009.0129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059303789"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.14806/ej.19.b.729", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1067372996"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2016-12", 
    "datePublishedReg": "2016-12-01", 
    "description": "BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples.\nDESCRIPTION: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned \"omics\" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations.\nCONCLUSIONS: Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s13326-016-0067-z", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2621826", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1043573", 
        "issn": [
          "2041-1480"
        ], 
        "name": "Journal of Biomedical Semantics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "7"
      }
    ], 
    "name": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation", 
    "pagination": "39", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "340d202264aabda1b741b431375459de4d1f7f225e5d7ec3ea95acb80af82228"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "27296299"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101531992"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s13326-016-0067-z"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1010925225"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s13326-016-0067-z", 
      "https://app.dimensions.ai/details/publication/pub.1010925225"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:27", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000362_0000000362/records_87119_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2Fs13326-016-0067-z"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13326-016-0067-z'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13326-016-0067-z'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13326-016-0067-z'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13326-016-0067-z'


 

This table displays all metadata directly associated to this object as RDF triples.

295 TRIPLES      21 PREDICATES      66 URIs      31 LITERALS      19 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s13326-016-0067-z schema:about N2b36db128b8a466f82fd2666ab01143b
2 N2edeec775f8f4ae3baa8f8d502aa70da
3 N3947d1c522584f07a1dcd58cb60b83df
4 N6b25eef6892843768f382d70e7a6f768
5 N96f8af7eb5494c2bb035f37d4f8fa432
6 N97c237c55b3843738e2143c43f7d6576
7 N9b296cadd9cd481b87537e81030558a4
8 Ndf685bf177554201bd693d7af081bb9b
9 Nef7afc4e38f84d91a3d6052a84c8b6a5
10 Nf7114d2b9a6f4ba39adc0b18b742087d
11 anzsrc-for:08
12 anzsrc-for:0806
13 schema:author N77e25a2b019f41738b85810053fd1654
14 schema:citation sg:pub.10.1186/2041-1480-1-8
15 sg:pub.10.1186/2041-1480-2-4
16 sg:pub.10.1186/2041-1480-2-6
17 sg:pub.10.1186/2041-1480-4-6
18 sg:pub.10.1186/2041-1480-5-5
19 sg:pub.10.1186/gb-2005-6-5-r44
20 sg:pub.10.1186/gb-2010-11-8-r88
21 https://doi.org/10.1021/ci100150d
22 https://doi.org/10.1042/bj0450563
23 https://doi.org/10.1089/omi.2009.0129
24 https://doi.org/10.1093/bioinformatics/btl647
25 https://doi.org/10.1093/bioinformatics/btm189
26 https://doi.org/10.1093/bioinformatics/btp163
27 https://doi.org/10.1093/bioinformatics/btq475
28 https://doi.org/10.1093/bioinformatics/bts494
29 https://doi.org/10.1093/glycob/cwj049
30 https://doi.org/10.1093/nar/gkq1014
31 https://doi.org/10.1093/nar/gkq733
32 https://doi.org/10.1093/nar/gks1068
33 https://doi.org/10.1093/nar/gks1152
34 https://doi.org/10.1093/nar/gks1175
35 https://doi.org/10.1093/nar/gks1195
36 https://doi.org/10.1093/nar/gkt1128
37 https://doi.org/10.1101/gr.094607.109
38 https://doi.org/10.1101/gr.361602
39 https://doi.org/10.14806/ej.19.b.729
40 https://doi.org/10.7717/peerj.933
41 schema:datePublished 2016-12
42 schema:datePublishedReg 2016-12-01
43 schema:description BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. DESCRIPTION: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. CONCLUSIONS: Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.
44 schema:genre research_article
45 schema:inLanguage en
46 schema:isAccessibleForFree true
47 schema:isPartOf N179e73b8fb2f4ed78c0c5cb3a8d4dcf2
48 Nadefd134b0304f34b801dccef05ae252
49 sg:journal.1043573
50 schema:name FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
51 schema:pagination 39
52 schema:productId N7a738a6b8f0d48b783cdabfb50a5ef72
53 Nd210d4c154044d1999245002c05808f3
54 Ne407399b8fa947ce9d38ee6a5260c09e
55 Ne445e109ede24f1b910627bdd119e83d
56 Ne78276db7c0c46f9bb66a4f54551dbef
57 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010925225
58 https://doi.org/10.1186/s13326-016-0067-z
59 schema:sdDatePublished 2019-04-11T12:27
60 schema:sdLicense https://scigraph.springernature.com/explorer/license/
61 schema:sdPublisher N57d9819e9e9347dcb084617e72663935
62 schema:url https://link.springer.com/10.1186%2Fs13326-016-0067-z
63 sgo:license sg:explorer/license/
64 sgo:sdDataset articles
65 rdf:type schema:ScholarlyArticle
66 N179e73b8fb2f4ed78c0c5cb3a8d4dcf2 schema:volumeNumber 7
67 rdf:type schema:PublicationVolume
68 N26dc55a1d9f347d0b70da8c96f0bce01 schema:name Department of Computer Science, SY23 3DB, Aberystwyth, UK
69 rdf:type schema:Organization
70 N2b36db128b8a466f82fd2666ab01143b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name Proteins
72 rdf:type schema:DefinedTerm
73 N2edeec775f8f4ae3baa8f8d502aa70da schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Databases, Protein
75 rdf:type schema:DefinedTerm
76 N346a35ae87304af1b064e66ee380e8ea schema:name CODAMONO, 5-121 Marion Street, M6R 1E6, Toronto, Ontario, Canada
77 rdf:type schema:Organization
78 N3947d1c522584f07a1dcd58cb60b83df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
79 schema:name Databases, Genetic
80 rdf:type schema:DefinedTerm
81 N3a4a4ded8c254ff4be5d7d26c547aaed rdf:first sg:person.0712511300.60
82 rdf:rest N91791a57d28b4450870c3c09f2120d53
83 N4863b1d59a194c0284bbca6aca5ed478 rdf:first sg:person.01150006507.62
84 rdf:rest rdf:nil
85 N57d9819e9e9347dcb084617e72663935 schema:name Springer Nature - SN SciGraph project
86 rdf:type schema:Organization
87 N5ad2d0f981e244099c57c89785ed1875 rdf:first sg:person.012665544347.43
88 rdf:rest N3a4a4ded8c254ff4be5d7d26c547aaed
89 N6b25eef6892843768f382d70e7a6f768 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
90 schema:name Biological Ontologies
91 rdf:type schema:DefinedTerm
92 N77e25a2b019f41738b85810053fd1654 rdf:first sg:person.01300247434.89
93 rdf:rest N91e362a3355b475291d8fc0c839544f6
94 N7a738a6b8f0d48b783cdabfb50a5ef72 schema:name nlm_unique_id
95 schema:value 101531992
96 rdf:type schema:PropertyValue
97 N916bcd7081154ad6a37ce65a4abc3e09 rdf:first sg:person.01324655201.14
98 rdf:rest N5ad2d0f981e244099c57c89785ed1875
99 N91791a57d28b4450870c3c09f2120d53 rdf:first sg:person.01300743466.43
100 rdf:rest Nba7b506fa1424a80a08cb29daffc0c26
101 N91e362a3355b475291d8fc0c839544f6 rdf:first sg:person.011151027407.17
102 rdf:rest Nf4e71700950e4acfa11a8b0ab5e03202
103 N96f8af7eb5494c2bb035f37d4f8fa432 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Humans
105 rdf:type schema:DefinedTerm
106 N97c237c55b3843738e2143c43f7d6576 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Semantics
108 rdf:type schema:DefinedTerm
109 N9b296cadd9cd481b87537e81030558a4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Nucleotides
111 rdf:type schema:DefinedTerm
112 Nadefd134b0304f34b801dccef05ae252 schema:issueNumber 1
113 rdf:type schema:PublicationIssue
114 Nba7b506fa1424a80a08cb29daffc0c26 rdf:first sg:person.0775625561.49
115 rdf:rest Nbf73345a0ca34baeb2ec3a680bbbe4e1
116 Nbf73345a0ca34baeb2ec3a680bbbe4e1 rdf:first sg:person.01237652002.94
117 rdf:rest N4863b1d59a194c0284bbca6aca5ed478
118 Nd210d4c154044d1999245002c05808f3 schema:name doi
119 schema:value 10.1186/s13326-016-0067-z
120 rdf:type schema:PropertyValue
121 Nde7b4071431a40deb8c4ecce3f829aac rdf:first sg:person.0660120074.62
122 rdf:rest N916bcd7081154ad6a37ce65a4abc3e09
123 Ndf685bf177554201bd693d7af081bb9b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Fuzzy Logic
125 rdf:type schema:DefinedTerm
126 Ne407399b8fa947ce9d38ee6a5260c09e schema:name dimensions_id
127 schema:value pub.1010925225
128 rdf:type schema:PropertyValue
129 Ne445e109ede24f1b910627bdd119e83d schema:name readcube_id
130 schema:value 340d202264aabda1b741b431375459de4d1f7f225e5d7ec3ea95acb80af82228
131 rdf:type schema:PropertyValue
132 Ne78276db7c0c46f9bb66a4f54551dbef schema:name pubmed_id
133 schema:value 27296299
134 rdf:type schema:PropertyValue
135 Nef7afc4e38f84d91a3d6052a84c8b6a5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Molecular Sequence Annotation
137 rdf:type schema:DefinedTerm
138 Nf389b3d161a04956b477f106ec3929aa schema:name Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, 94305-5479, Stanford, CA, US
139 rdf:type schema:Organization
140 Nf4e71700950e4acfa11a8b0ab5e03202 rdf:first sg:person.01320675003.14
141 rdf:rest Nde7b4071431a40deb8c4ecce3f829aac
142 Nf7114d2b9a6f4ba39adc0b18b742087d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Reference Books
144 rdf:type schema:DefinedTerm
145 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
146 schema:name Information and Computing Sciences
147 rdf:type schema:DefinedTerm
148 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
149 schema:name Information Systems
150 rdf:type schema:DefinedTerm
151 sg:grant.2621826 http://pending.schema.org/fundedItem sg:pub.10.1186/s13326-016-0067-z
152 rdf:type schema:MonetaryGrant
153 sg:journal.1043573 schema:issn 2041-1480
154 schema:name Journal of Biomedical Semantics
155 rdf:type schema:Periodical
156 sg:person.011151027407.17 schema:affiliation https://www.grid.ac/institutes/grid.184769.5
157 schema:familyName Mungall
158 schema:givenName Christopher J.
159 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011151027407.17
160 rdf:type schema:Person
161 sg:person.01150006507.62 schema:affiliation https://www.grid.ac/institutes/grid.43641.34
162 schema:familyName Cock
163 schema:givenName Peter J. A.
164 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150006507.62
165 rdf:type schema:Person
166 sg:person.01237652002.94 schema:affiliation https://www.grid.ac/institutes/grid.418987.b
167 schema:familyName Katayama
168 schema:givenName Toshiaki
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01237652002.94
170 rdf:type schema:Person
171 sg:person.012665544347.43 schema:affiliation https://www.grid.ac/institutes/grid.428717.f
172 schema:familyName Bonnal
173 schema:givenName Raoul J. P.
174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012665544347.43
175 rdf:type schema:Person
176 sg:person.01300247434.89 schema:affiliation https://www.grid.ac/institutes/grid.419765.8
177 schema:familyName Bolleman
178 schema:givenName Jerven T.
179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300247434.89
180 rdf:type schema:Person
181 sg:person.01300743466.43 schema:affiliation N26dc55a1d9f347d0b70da8c96f0bce01
182 schema:familyName Hoehndorf
183 schema:givenName Robert
184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300743466.43
185 rdf:type schema:Person
186 sg:person.01320675003.14 schema:affiliation https://www.grid.ac/institutes/grid.425375.2
187 schema:familyName Strozzi
188 schema:givenName Francesco
189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320675003.14
190 rdf:type schema:Person
191 sg:person.01324655201.14 schema:affiliation Nf389b3d161a04956b477f106ec3929aa
192 schema:familyName Dumontier
193 schema:givenName Michel
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01324655201.14
195 rdf:type schema:Person
196 sg:person.0660120074.62 schema:affiliation N346a35ae87304af1b064e66ee380e8ea
197 schema:familyName Baran
198 schema:givenName Joachim
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0660120074.62
200 rdf:type schema:Person
201 sg:person.0712511300.60 schema:affiliation https://www.grid.ac/institutes/grid.47840.3f
202 schema:familyName Buels
203 schema:givenName Robert
204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712511300.60
205 rdf:type schema:Person
206 sg:person.0775625561.49 schema:affiliation https://www.grid.ac/institutes/grid.288127.6
207 schema:familyName Fujisawa
208 schema:givenName Takatomo
209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775625561.49
210 rdf:type schema:Person
211 sg:pub.10.1186/2041-1480-1-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008414706
212 https://doi.org/10.1186/2041-1480-1-8
213 rdf:type schema:CreativeWork
214 sg:pub.10.1186/2041-1480-2-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008246254
215 https://doi.org/10.1186/2041-1480-2-4
216 rdf:type schema:CreativeWork
217 sg:pub.10.1186/2041-1480-2-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004132434
218 https://doi.org/10.1186/2041-1480-2-6
219 rdf:type schema:CreativeWork
220 sg:pub.10.1186/2041-1480-4-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016886003
221 https://doi.org/10.1186/2041-1480-4-6
222 rdf:type schema:CreativeWork
223 sg:pub.10.1186/2041-1480-5-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046582343
224 https://doi.org/10.1186/2041-1480-5-5
225 rdf:type schema:CreativeWork
226 sg:pub.10.1186/gb-2005-6-5-r44 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026484271
227 https://doi.org/10.1186/gb-2005-6-5-r44
228 rdf:type schema:CreativeWork
229 sg:pub.10.1186/gb-2010-11-8-r88 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025532561
230 https://doi.org/10.1186/gb-2010-11-8-r88
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1021/ci100150d schema:sameAs https://app.dimensions.ai/details/publication/pub.1055402421
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1042/bj0450563 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026481020
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1089/omi.2009.0129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059303789
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1093/bioinformatics/btl647 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000310618
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1093/bioinformatics/btm189 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051261157
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/bioinformatics/btp163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011232850
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1093/bioinformatics/btq475 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033174360
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1093/bioinformatics/bts494 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030116406
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1093/glycob/cwj049 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002645985
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1093/nar/gkq1014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037469099
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1093/nar/gkq733 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048436860
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1093/nar/gks1068 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000076796
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1093/nar/gks1152 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004169169
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1093/nar/gks1175 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024766283
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1093/nar/gks1195 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035881992
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1093/nar/gkt1128 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007987025
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1101/gr.094607.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010225667
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1101/gr.361602 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028020859
267 rdf:type schema:CreativeWork
268 https://doi.org/10.14806/ej.19.b.729 schema:sameAs https://app.dimensions.ai/details/publication/pub.1067372996
269 rdf:type schema:CreativeWork
270 https://doi.org/10.7717/peerj.933 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009614731
271 rdf:type schema:CreativeWork
272 https://www.grid.ac/institutes/grid.184769.5 schema:alternateName Lawrence Berkeley National Laboratory
273 schema:name Genomics Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, US
274 rdf:type schema:Organization
275 https://www.grid.ac/institutes/grid.288127.6 schema:alternateName National Institute of Genetics
276 schema:name Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-08540, Shizuoka, Japan
277 rdf:type schema:Organization
278 https://www.grid.ac/institutes/grid.418987.b schema:alternateName Research Organization of Information and Systems
279 schema:name Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan
280 rdf:type schema:Organization
281 https://www.grid.ac/institutes/grid.419765.8 schema:alternateName Swiss Institute of Bioinformatics
282 schema:name Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel, Servet, 1211, Geneva 4, Switzerland
283 rdf:type schema:Organization
284 https://www.grid.ac/institutes/grid.425375.2 schema:alternateName Parco Tecnologico Padano
285 schema:name CeRSA, Parco Tecnologico Padano, 26900, Lodi, Italy
286 rdf:type schema:Organization
287 https://www.grid.ac/institutes/grid.428717.f schema:alternateName Istituto Nazionale Genetica Molecolare
288 schema:name Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy
289 rdf:type schema:Organization
290 https://www.grid.ac/institutes/grid.43641.34 schema:alternateName James Hutton Institute
291 schema:name The James Hutton Institute, DD2 5DA, Dundee, UK
292 rdf:type schema:Organization
293 https://www.grid.ac/institutes/grid.47840.3f schema:alternateName University of California, Berkeley
294 schema:name University of California, Berkeley, Berkeley, CA, USA
295 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...