Sensing the cilium, digital capture of ciliary data for comparative genomics investigations View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Karen R. Christie, Judith A. Blake

ABSTRACT

Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work. Methods: We focused on the capture of information about cilia as studied in the laboratory mouse, a primary model of human biology. The workflow developed establishes a standard for capture of comparative functional data relevant to human biology. We established the 310 closest mouse orthologs of the 302 human genes defined in the SYSCILIA Gold Standard set of ciliary genes. For the mouse genes, we identified biomedical literature for curation and used Gene Ontology (GO) curation paradigms to provide functional annotations from these publications. Results: Employing a methodology for comprehensive capture of experimental data about cilia genes in structured, digital form, we established a workflow for curation of experimental literature detailing molecular function and roles of cilia proteins starting with the mouse orthologs of the human SYSCILIA gene set. We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO. During the time frame of the ontology improvement project, we have fully curated 134 of these 310 mouse genes, resulting in an increase in the number of ciliary and other experimental annotations. Conclusions: We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium's Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses. More... »

PAGES

3

References to SciGraph publications

  • 2012-12. Photoreceptor sensory cilia and ciliopathies: focus on CEP290, RPGR and their interacting proteins in CILIA
  • 2013-08. Large-scale gene function analysis with the PANTHER classification system in NATURE PROTOCOLS
  • 2016-02. The axoneme: the propulsive engine of spermatozoa and cilia and associated ciliopathies leading to infertility in JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
  • 2015-10. Visual annotation display (VLAD): a tool for finding functional themes in lists of genes in MAMMALIAN GENOME
  • 2015-12. Situs inversus and ciliary abnormalities: 20 years later, what is the connection? in CILIA
  • 2011-07. Ciliopathies: an expanding disease spectrum in PEDIATRIC NEPHROLOGY
  • 2017-12. The Gene Ontology of eukaryotic cilia and flagella in CILIA
  • 2015-05. Global genetic analysis in mice unveils central role for cilia in congenital heart disease in NATURE
  • 2013-12. The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium in CILIA
  • 2015-12. Ciliopathies - from rare inherited cystic kidney diseases to basic cellular function in MOLECULAR AND CELLULAR PEDIATRICS
  • 2015-10. Application of comparative biology in GO functional annotation: the mouse model in MAMMALIAN GENOME
  • 2015-08. MouseMine: a new data warehouse for MGI in MAMMALIAN GENOME
  • 2009-06. The nonmotile ciliopathies in GENETICS IN MEDICINE
  • 2009-12. The dynamic cilium in human diseases in PATHOGENETICS
  • 2014-12. Remodeling Cildb, a popular database for cilia and links for ciliopathies in CILIA
  • 2015-08. Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis in MAMMALIAN GENOME
  • Journal

    TITLE

    Cilia

    ISSUE

    1

    VOLUME

    7

    Author Affiliations

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13630-018-0057-0

    DOI

    http://dx.doi.org/10.1186/s13630-018-0057-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1103456288

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29713460


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Jackson Laboratory", 
              "id": "https://www.grid.ac/institutes/grid.249880.f", 
              "name": [
                "The Jackson Laboratory, 600 Main Street, 04609, Bar Harbor, ME, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Christie", 
            "givenName": "Karen R.", 
            "id": "sg:person.01337345327.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337345327.03"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Jackson Laboratory", 
              "id": "https://www.grid.ac/institutes/grid.249880.f", 
              "name": [
                "The Jackson Laboratory, 600 Main Street, 04609, Bar Harbor, ME, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Blake", 
            "givenName": "Judith A.", 
            "id": "sg:person.01050533050.54", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050533050.54"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1002/0471250953.bi0129s53", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000113515"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/2046-2530-3-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001755658", 
              "https://doi.org/10.1186/2046-2530-3-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-genet-111212-133243", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002226280"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-genet-111212-133243", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002226280"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gku1179", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004916975"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1586/ers.12.60", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007917406"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9573-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008025003", 
              "https://doi.org/10.1007/s00335-015-9573-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9573-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008025003", 
              "https://doi.org/10.1007/s00335-015-9573-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkn803", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008205393"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tins.2016.05.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008649456"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature14269", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011106132", 
              "https://doi.org/10.1038/nature14269"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/biosci/biu174", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011249696"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1083/jcb.201001138", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012073317"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0091-679x(08)94001-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015334300"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1097/gim.0b013e3181a02882", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018171230", 
              "https://doi.org/10.1097/gim.0b013e3181a02882"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1097/gim.0b013e3181a02882", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018171230", 
              "https://doi.org/10.1097/gim.0b013e3181a02882"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1242/dmm.009340", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019295160"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gku989", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020681127"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1097/mnh.0b013e3283520f17", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021068289"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1097/mnh.0b013e3283520f17", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021068289"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bdrc.21067", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025479060"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.7554/elife.11066", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025972722"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9582-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026707873", 
              "https://doi.org/10.1007/s00335-015-9582-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9582-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026707873", 
              "https://doi.org/10.1007/s00335-015-9582-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00467-010-1731-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027956749", 
              "https://doi.org/10.1007/s00467-010-1731-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1399-0004.2009.01305.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028291445"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1399-0004.2009.01305.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028291445"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.073585.107", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029032167"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1152/ajprenal.00399.2013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029274144"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1242/jcs.066308", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029310244"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/hmg/ddv137", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030779664"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/hmg/ddv137", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030779664"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/2046-2530-2-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033096337", 
              "https://doi.org/10.1186/2046-2530-2-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2013.092", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033211555", 
              "https://doi.org/10.1038/nprot.2013.092"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2013.092", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033211555", 
              "https://doi.org/10.1038/nprot.2013.092"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9570-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036849009", 
              "https://doi.org/10.1007/s00335-015-9570-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9570-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036849009", 
              "https://doi.org/10.1007/s00335-015-9570-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13630-014-0010-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037054519", 
              "https://doi.org/10.1186/s13630-014-0010-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13630-014-0010-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037054519", 
              "https://doi.org/10.1186/s13630-014-0010-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.12703/p7-36", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037345247"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkv1290", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037647823"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s40348-015-0019-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037934408", 
              "https://doi.org/10.1186/s40348-015-0019-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s40348-015-0019-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037934408", 
              "https://doi.org/10.1186/s40348-015-0019-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0070-2153(08)00813-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038330145"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/wdev.199", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038932445"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1755-8417-2-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039522645", 
              "https://doi.org/10.1186/1755-8417-2-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.3390/cells4030500", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040578776"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10815-016-0652-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042423091", 
              "https://doi.org/10.1007/s10815-016-0652-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10815-016-0652-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042423091", 
              "https://doi.org/10.1007/s10815-016-0652-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bib/bbr042", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043299266"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1017/s0007114516002282", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043793889"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.prrv.2009.02.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044471217"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/2046-2530-1-22", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044874218", 
              "https://doi.org/10.1186/2046-2530-1-22"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1677/joe-09-0116", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045227389"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-physiol-021014-071931", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050614620"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9580-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050920185", 
              "https://doi.org/10.1007/s00335-015-9580-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00335-015-9580-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050920185", 
              "https://doi.org/10.1007/s00335-015-9580-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.diff.2011.11.002", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051644994"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/database/bas045", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052477055"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/humrep/dev227", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1059648599"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/scisignal.285pt5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062684319"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/org.26710", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1072306789"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/org.27483", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1072306796"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/9780471650126.dob0273.pub2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1089871629"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13630-017-0054-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092706182", 
              "https://doi.org/10.1186/s13630-017-0054-8"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-12", 
        "datePublishedReg": "2018-12-01", 
        "description": "Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work.\nMethods: We focused on the capture of information about cilia as studied in the laboratory mouse, a primary model of human biology. The workflow developed establishes a standard for capture of comparative functional data relevant to human biology. We established the 310 closest mouse orthologs of the 302 human genes defined in the SYSCILIA Gold Standard set of ciliary genes. For the mouse genes, we identified biomedical literature for curation and used Gene Ontology (GO) curation paradigms to provide functional annotations from these publications.\nResults: Employing a methodology for comprehensive capture of experimental data about cilia genes in structured, digital form, we established a workflow for curation of experimental literature detailing molecular function and roles of cilia proteins starting with the mouse orthologs of the human SYSCILIA gene set. We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO. During the time frame of the ontology improvement project, we have fully curated 134 of these 310 mouse genes, resulting in an increase in the number of ciliary and other experimental annotations.\nConclusions: We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium's Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/s13630-018-0057-0", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2436658", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2529094", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2697599", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2439779", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2697596", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2439767", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1046983", 
            "issn": [
              "2046-2530"
            ], 
            "name": "Cilia", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "7"
          }
        ], 
        "name": "Sensing the cilium, digital capture of ciliary data for comparative genomics investigations", 
        "pagination": "3", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "3330966eb34e5aeaf9498037513c0356f83a8147056d36c41a34576c60769ab2"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "29713460"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101585639"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13630-018-0057-0"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1103456288"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13630-018-0057-0", 
          "https://app.dimensions.ai/details/publication/pub.1103456288"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-11T09:40", 
        "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/v90/0000000346_0000000346/records_99839_00000004.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://link.springer.com/10.1186%2Fs13630-018-0057-0"
      }
    ]
     

    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/s13630-018-0057-0'

    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/s13630-018-0057-0'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13630-018-0057-0'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13630-018-0057-0'


     

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

    259 TRIPLES      21 PREDICATES      81 URIs      21 LITERALS      9 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13630-018-0057-0 schema:about anzsrc-for:06
    2 anzsrc-for:0604
    3 schema:author N753a3a06c7674348b60be6d1ea81160e
    4 schema:citation sg:pub.10.1007/s00335-015-9570-2
    5 sg:pub.10.1007/s00335-015-9573-z
    6 sg:pub.10.1007/s00335-015-9580-0
    7 sg:pub.10.1007/s00335-015-9582-y
    8 sg:pub.10.1007/s00467-010-1731-7
    9 sg:pub.10.1007/s10815-016-0652-1
    10 sg:pub.10.1038/nature14269
    11 sg:pub.10.1038/nprot.2013.092
    12 sg:pub.10.1097/gim.0b013e3181a02882
    13 sg:pub.10.1186/1755-8417-2-3
    14 sg:pub.10.1186/2046-2530-1-22
    15 sg:pub.10.1186/2046-2530-2-7
    16 sg:pub.10.1186/2046-2530-3-9
    17 sg:pub.10.1186/s13630-014-0010-9
    18 sg:pub.10.1186/s13630-017-0054-8
    19 sg:pub.10.1186/s40348-015-0019-1
    20 https://doi.org/10.1002/0471250953.bi0129s53
    21 https://doi.org/10.1002/9780471650126.dob0273.pub2
    22 https://doi.org/10.1002/bdrc.21067
    23 https://doi.org/10.1002/wdev.199
    24 https://doi.org/10.1016/j.diff.2011.11.002
    25 https://doi.org/10.1016/j.prrv.2009.02.001
    26 https://doi.org/10.1016/j.tins.2016.05.004
    27 https://doi.org/10.1016/s0070-2153(08)00813-2
    28 https://doi.org/10.1016/s0091-679x(08)94001-2
    29 https://doi.org/10.1017/s0007114516002282
    30 https://doi.org/10.1083/jcb.201001138
    31 https://doi.org/10.1093/bib/bbr042
    32 https://doi.org/10.1093/biosci/biu174
    33 https://doi.org/10.1093/database/bas045
    34 https://doi.org/10.1093/hmg/ddv137
    35 https://doi.org/10.1093/humrep/dev227
    36 https://doi.org/10.1093/nar/gkn803
    37 https://doi.org/10.1093/nar/gku1179
    38 https://doi.org/10.1093/nar/gku989
    39 https://doi.org/10.1093/nar/gkv1290
    40 https://doi.org/10.1097/mnh.0b013e3283520f17
    41 https://doi.org/10.1101/gr.073585.107
    42 https://doi.org/10.1111/j.1399-0004.2009.01305.x
    43 https://doi.org/10.1126/scisignal.285pt5
    44 https://doi.org/10.1146/annurev-genet-111212-133243
    45 https://doi.org/10.1146/annurev-physiol-021014-071931
    46 https://doi.org/10.1152/ajprenal.00399.2013
    47 https://doi.org/10.1242/dmm.009340
    48 https://doi.org/10.1242/jcs.066308
    49 https://doi.org/10.12703/p7-36
    50 https://doi.org/10.1586/ers.12.60
    51 https://doi.org/10.1677/joe-09-0116
    52 https://doi.org/10.3390/cells4030500
    53 https://doi.org/10.4161/org.26710
    54 https://doi.org/10.4161/org.27483
    55 https://doi.org/10.7554/elife.11066
    56 schema:datePublished 2018-12
    57 schema:datePublishedReg 2018-12-01
    58 schema:description Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work. Methods: We focused on the capture of information about cilia as studied in the laboratory mouse, a primary model of human biology. The workflow developed establishes a standard for capture of comparative functional data relevant to human biology. We established the 310 closest mouse orthologs of the 302 human genes defined in the SYSCILIA Gold Standard set of ciliary genes. For the mouse genes, we identified biomedical literature for curation and used Gene Ontology (GO) curation paradigms to provide functional annotations from these publications. Results: Employing a methodology for comprehensive capture of experimental data about cilia genes in structured, digital form, we established a workflow for curation of experimental literature detailing molecular function and roles of cilia proteins starting with the mouse orthologs of the human SYSCILIA gene set. We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO. During the time frame of the ontology improvement project, we have fully curated 134 of these 310 mouse genes, resulting in an increase in the number of ciliary and other experimental annotations. Conclusions: We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium's Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses.
    59 schema:genre research_article
    60 schema:inLanguage en
    61 schema:isAccessibleForFree true
    62 schema:isPartOf N4c2b308760504319ac8bfa550d856bfd
    63 Ne6cc01ecf65c4d76892630cf076ca268
    64 sg:journal.1046983
    65 schema:name Sensing the cilium, digital capture of ciliary data for comparative genomics investigations
    66 schema:pagination 3
    67 schema:productId N5220a3fcbd614349a99818054eb8c886
    68 N5c9aa55bc5d64d09b867151daf1311bf
    69 N61e8109747c549e19ab37479775c6bb4
    70 Nb10b41ac07284d46aea0793fc83bec9f
    71 Ne7fe770ce8e14fdfa1679f8ebebf24cd
    72 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103456288
    73 https://doi.org/10.1186/s13630-018-0057-0
    74 schema:sdDatePublished 2019-04-11T09:40
    75 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    76 schema:sdPublisher N821d9b05010145479cd22655a4061a4d
    77 schema:url https://link.springer.com/10.1186%2Fs13630-018-0057-0
    78 sgo:license sg:explorer/license/
    79 sgo:sdDataset articles
    80 rdf:type schema:ScholarlyArticle
    81 N4c2b308760504319ac8bfa550d856bfd schema:volumeNumber 7
    82 rdf:type schema:PublicationVolume
    83 N5220a3fcbd614349a99818054eb8c886 schema:name pubmed_id
    84 schema:value 29713460
    85 rdf:type schema:PropertyValue
    86 N5c9aa55bc5d64d09b867151daf1311bf schema:name readcube_id
    87 schema:value 3330966eb34e5aeaf9498037513c0356f83a8147056d36c41a34576c60769ab2
    88 rdf:type schema:PropertyValue
    89 N61e8109747c549e19ab37479775c6bb4 schema:name dimensions_id
    90 schema:value pub.1103456288
    91 rdf:type schema:PropertyValue
    92 N753a3a06c7674348b60be6d1ea81160e rdf:first sg:person.01337345327.03
    93 rdf:rest Nc3db07d0c9ac446b94d98c1f75b2b864
    94 N821d9b05010145479cd22655a4061a4d schema:name Springer Nature - SN SciGraph project
    95 rdf:type schema:Organization
    96 Nb10b41ac07284d46aea0793fc83bec9f schema:name doi
    97 schema:value 10.1186/s13630-018-0057-0
    98 rdf:type schema:PropertyValue
    99 Nc3db07d0c9ac446b94d98c1f75b2b864 rdf:first sg:person.01050533050.54
    100 rdf:rest rdf:nil
    101 Ne6cc01ecf65c4d76892630cf076ca268 schema:issueNumber 1
    102 rdf:type schema:PublicationIssue
    103 Ne7fe770ce8e14fdfa1679f8ebebf24cd schema:name nlm_unique_id
    104 schema:value 101585639
    105 rdf:type schema:PropertyValue
    106 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    107 schema:name Biological Sciences
    108 rdf:type schema:DefinedTerm
    109 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    110 schema:name Genetics
    111 rdf:type schema:DefinedTerm
    112 sg:grant.2436658 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    113 rdf:type schema:MonetaryGrant
    114 sg:grant.2439767 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    115 rdf:type schema:MonetaryGrant
    116 sg:grant.2439779 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    117 rdf:type schema:MonetaryGrant
    118 sg:grant.2529094 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    119 rdf:type schema:MonetaryGrant
    120 sg:grant.2697596 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    121 rdf:type schema:MonetaryGrant
    122 sg:grant.2697599 http://pending.schema.org/fundedItem sg:pub.10.1186/s13630-018-0057-0
    123 rdf:type schema:MonetaryGrant
    124 sg:journal.1046983 schema:issn 2046-2530
    125 schema:name Cilia
    126 rdf:type schema:Periodical
    127 sg:person.01050533050.54 schema:affiliation https://www.grid.ac/institutes/grid.249880.f
    128 schema:familyName Blake
    129 schema:givenName Judith A.
    130 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050533050.54
    131 rdf:type schema:Person
    132 sg:person.01337345327.03 schema:affiliation https://www.grid.ac/institutes/grid.249880.f
    133 schema:familyName Christie
    134 schema:givenName Karen R.
    135 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337345327.03
    136 rdf:type schema:Person
    137 sg:pub.10.1007/s00335-015-9570-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036849009
    138 https://doi.org/10.1007/s00335-015-9570-2
    139 rdf:type schema:CreativeWork
    140 sg:pub.10.1007/s00335-015-9573-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1008025003
    141 https://doi.org/10.1007/s00335-015-9573-z
    142 rdf:type schema:CreativeWork
    143 sg:pub.10.1007/s00335-015-9580-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050920185
    144 https://doi.org/10.1007/s00335-015-9580-0
    145 rdf:type schema:CreativeWork
    146 sg:pub.10.1007/s00335-015-9582-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1026707873
    147 https://doi.org/10.1007/s00335-015-9582-y
    148 rdf:type schema:CreativeWork
    149 sg:pub.10.1007/s00467-010-1731-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027956749
    150 https://doi.org/10.1007/s00467-010-1731-7
    151 rdf:type schema:CreativeWork
    152 sg:pub.10.1007/s10815-016-0652-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042423091
    153 https://doi.org/10.1007/s10815-016-0652-1
    154 rdf:type schema:CreativeWork
    155 sg:pub.10.1038/nature14269 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011106132
    156 https://doi.org/10.1038/nature14269
    157 rdf:type schema:CreativeWork
    158 sg:pub.10.1038/nprot.2013.092 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033211555
    159 https://doi.org/10.1038/nprot.2013.092
    160 rdf:type schema:CreativeWork
    161 sg:pub.10.1097/gim.0b013e3181a02882 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018171230
    162 https://doi.org/10.1097/gim.0b013e3181a02882
    163 rdf:type schema:CreativeWork
    164 sg:pub.10.1186/1755-8417-2-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039522645
    165 https://doi.org/10.1186/1755-8417-2-3
    166 rdf:type schema:CreativeWork
    167 sg:pub.10.1186/2046-2530-1-22 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044874218
    168 https://doi.org/10.1186/2046-2530-1-22
    169 rdf:type schema:CreativeWork
    170 sg:pub.10.1186/2046-2530-2-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033096337
    171 https://doi.org/10.1186/2046-2530-2-7
    172 rdf:type schema:CreativeWork
    173 sg:pub.10.1186/2046-2530-3-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001755658
    174 https://doi.org/10.1186/2046-2530-3-9
    175 rdf:type schema:CreativeWork
    176 sg:pub.10.1186/s13630-014-0010-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037054519
    177 https://doi.org/10.1186/s13630-014-0010-9
    178 rdf:type schema:CreativeWork
    179 sg:pub.10.1186/s13630-017-0054-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092706182
    180 https://doi.org/10.1186/s13630-017-0054-8
    181 rdf:type schema:CreativeWork
    182 sg:pub.10.1186/s40348-015-0019-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037934408
    183 https://doi.org/10.1186/s40348-015-0019-1
    184 rdf:type schema:CreativeWork
    185 https://doi.org/10.1002/0471250953.bi0129s53 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000113515
    186 rdf:type schema:CreativeWork
    187 https://doi.org/10.1002/9780471650126.dob0273.pub2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1089871629
    188 rdf:type schema:CreativeWork
    189 https://doi.org/10.1002/bdrc.21067 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025479060
    190 rdf:type schema:CreativeWork
    191 https://doi.org/10.1002/wdev.199 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038932445
    192 rdf:type schema:CreativeWork
    193 https://doi.org/10.1016/j.diff.2011.11.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051644994
    194 rdf:type schema:CreativeWork
    195 https://doi.org/10.1016/j.prrv.2009.02.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044471217
    196 rdf:type schema:CreativeWork
    197 https://doi.org/10.1016/j.tins.2016.05.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008649456
    198 rdf:type schema:CreativeWork
    199 https://doi.org/10.1016/s0070-2153(08)00813-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038330145
    200 rdf:type schema:CreativeWork
    201 https://doi.org/10.1016/s0091-679x(08)94001-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015334300
    202 rdf:type schema:CreativeWork
    203 https://doi.org/10.1017/s0007114516002282 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043793889
    204 rdf:type schema:CreativeWork
    205 https://doi.org/10.1083/jcb.201001138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012073317
    206 rdf:type schema:CreativeWork
    207 https://doi.org/10.1093/bib/bbr042 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043299266
    208 rdf:type schema:CreativeWork
    209 https://doi.org/10.1093/biosci/biu174 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011249696
    210 rdf:type schema:CreativeWork
    211 https://doi.org/10.1093/database/bas045 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052477055
    212 rdf:type schema:CreativeWork
    213 https://doi.org/10.1093/hmg/ddv137 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030779664
    214 rdf:type schema:CreativeWork
    215 https://doi.org/10.1093/humrep/dev227 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059648599
    216 rdf:type schema:CreativeWork
    217 https://doi.org/10.1093/nar/gkn803 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008205393
    218 rdf:type schema:CreativeWork
    219 https://doi.org/10.1093/nar/gku1179 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004916975
    220 rdf:type schema:CreativeWork
    221 https://doi.org/10.1093/nar/gku989 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020681127
    222 rdf:type schema:CreativeWork
    223 https://doi.org/10.1093/nar/gkv1290 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037647823
    224 rdf:type schema:CreativeWork
    225 https://doi.org/10.1097/mnh.0b013e3283520f17 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021068289
    226 rdf:type schema:CreativeWork
    227 https://doi.org/10.1101/gr.073585.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029032167
    228 rdf:type schema:CreativeWork
    229 https://doi.org/10.1111/j.1399-0004.2009.01305.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1028291445
    230 rdf:type schema:CreativeWork
    231 https://doi.org/10.1126/scisignal.285pt5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062684319
    232 rdf:type schema:CreativeWork
    233 https://doi.org/10.1146/annurev-genet-111212-133243 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002226280
    234 rdf:type schema:CreativeWork
    235 https://doi.org/10.1146/annurev-physiol-021014-071931 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050614620
    236 rdf:type schema:CreativeWork
    237 https://doi.org/10.1152/ajprenal.00399.2013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029274144
    238 rdf:type schema:CreativeWork
    239 https://doi.org/10.1242/dmm.009340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019295160
    240 rdf:type schema:CreativeWork
    241 https://doi.org/10.1242/jcs.066308 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029310244
    242 rdf:type schema:CreativeWork
    243 https://doi.org/10.12703/p7-36 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037345247
    244 rdf:type schema:CreativeWork
    245 https://doi.org/10.1586/ers.12.60 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007917406
    246 rdf:type schema:CreativeWork
    247 https://doi.org/10.1677/joe-09-0116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045227389
    248 rdf:type schema:CreativeWork
    249 https://doi.org/10.3390/cells4030500 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040578776
    250 rdf:type schema:CreativeWork
    251 https://doi.org/10.4161/org.26710 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072306789
    252 rdf:type schema:CreativeWork
    253 https://doi.org/10.4161/org.27483 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072306796
    254 rdf:type schema:CreativeWork
    255 https://doi.org/10.7554/elife.11066 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025972722
    256 rdf:type schema:CreativeWork
    257 https://www.grid.ac/institutes/grid.249880.f schema:alternateName Jackson Laboratory
    258 schema:name The Jackson Laboratory, 600 Main Street, 04609, Bar Harbor, ME, USA
    259 rdf:type schema:Organization
     




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


    ...