Gerar exemplo manualmente de nanopublicação do Trypanossoma Cruzi

[andrecsq]

O @MatheusFeijoo ficou responsável por fazer isso.

[andrecsq]

Do nosso papo de 15/10, entendemos melhor como funciona a nanopublicação.

Publicação mais atual explicando: https://arxiv.org/pdf/1809.06532.pdf

Exemplo figshare: https://figshare.com/articles/software/Gene-RD-provenance_V2_nanopublication/7931342

Guidelines: http://nanopub.org/guidelines/working_draft/ Exemplos http://server.np.scify.org/RAZMzdV6ee1H22zjChoboS2ZrCkj5fYXuUXu9Q1-kts3s http://server.np.scify.org/RAcqG_doyfOtYaezwsbioZ8ak7yTUhhIGEq1QJWjtkXD4

[andrecsq]

Eu e @MatheusFeijoo fizemos no dia 26/10 Input:

{
  "abstract": "Although the...",
  "keywords": [
    "Chagas disease",
    "PacBio",
    "Trypanosoma cruzi",
    "whole genome sequencing."
  ],
  "doi": "https://doi.org/10.1099/mgen.0.000177",
  "assembly": {
    "url": "https://www.ncbi.nlm.nih.gov/assembly/?linkname=pubmed_assembly\u0026from_uid=29708484",
    "links": [
      {
        "url": "https://www.ncbi.nlm.nih.gov/assembly/GCA_003177105.1",
        "report": {
          "organismName": "Trypanosoma cruzi (kinetoplastids)",
          "infraspecificName": "Strain: TCC",
          "bioSample": {
            "url": "https://www.ncbi.nlm.nih.gov/biosample/SAMN08458079/",
            "strain": "TCC",
            "collectionDate": "1982",
            "broadScaleEnvironmentalContext": "not applicable",
            "localScaleEnvironmentalContext": "not applicable",
            "environmentalMedium": "not applicable",
            "geographicLocation": "Argentina",
            "latLong": "34 S 59 W",
            "host": "Homo sapiens",
            "isolationAndGrowthCondition": "not applicable",
            "numberOfReplicons": "not applicable",
            "ploidy": "diploid",
            "propagation": "not applicable"
          },
          "submitter": "Institut Pasteur de Montevideo",
          "date": "2018/05/30",
          "ftpUrl": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/177/095/GCA_003177095.1_TCC_diploid_1.0",
          "gbffUrl": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/177/095/GCA_003177095.1_TCC_diploid_1.0/GCA_003177095.1_TCC_diploid_1.0_genomic.gbff.gz"
        }
      },
      {
        "url": "https://www.ncbi.nlm.nih.gov/assembly/GCA_003177095.1",
        "report": {
          "organismName": "Trypanosoma cruzi (kinetoplastids)",
          "infraspecificName": "Strain: TCC",
          "bioSample": {
            "url": "https://www.ncbi.nlm.nih.gov/biosample/SAMN08458079/",
            "strain": "TCC",
            "collectionDate": "1982",
            "broadScaleEnvironmentalContext": "not applicable",
            "localScaleEnvironmentalContext": "not applicable",
            "environmentalMedium": "not applicable",
            "geographicLocation": "Argentina",
            "latLong": "34 S 59 W",
            "host": "Homo sapiens",
            "isolationAndGrowthCondition": "not applicable",
            "numberOfReplicons": "not applicable",
            "ploidy": "diploid",
            "propagation": "not applicable"
          },
          "submitter": "Institut Pasteur de Montevideo",
          "date": "2018/05/30",
          "ftpUrl": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/177/095/GCA_003177095.1_TCC_diploid_1.0",
          "gbffUrl": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/177/095/GCA_003177095.1_TCC_diploid_1.0/GCA_003177095.1_TCC_diploid_1.0_genomic.gbff.gz"
        }
      }
    ]
  }
}

Esboço do output:

@prefix dc: <http://purl.org/dc/terms/> .
@prefix sub: <http://purl.org/np/RA1sViVmXf-W2aZW4Qk74KTaiD9gpLBPe2LhMsinHKKz8#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix pav: <http://purl.org/pav/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdfs: http://www.w3.org/2000/01/rdf-schema .
@prefix orcid: <https://orcid.org/> .
@prefix this: <http://example.org> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix ncbi-asb: <https://www.ncbi.nlm.nih.gov/assembly/>
@prefix biol: >https://ontologi.es/biol/ns.html>

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

sub:assertion {
  este assembly            é um  genoma
  ncbi-asb:GCA_003177105.1 a     sio:SIO_000984 ;
        se refere a    algo que  é um  organismo
        sio:SIO_000628 [         a     sio:SIO_010000 ;       
                                 tem taxonomia    <link>
                                 biol:hasTaxonomy <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=5693&lvl=3&lin=f&keep=1&srchmode=1&unlock> ;
                                 label doc <nome>                                 fim-algo
                                 dc:label  "Trypanosoma cruzi (kinetoplastids)" . ] .                     
}

sub:provenance {
  sub:assertion prov:hadPrimarySource <https://www.ncbi.nlm.nih.gov/biosample/SAMN08458079/> ;
    prov:wasAttributedTo "Institut Pasteur de Montevideo" ;        // como identificar instituicao unicamente? ainda não sabemos
    prov:collectedDate "1988-03-01T00:00:00+00:00"^^xsd:dateTime ;
    has evidence   <publication_link>
    sio:SIO_000772 <https://doi.org/10.1099/mgen.0.000177> ;
    aqui seria a data de submissão
    dc:created "2018-05-30T00:00:00+00:00"^^xsd:dateTime .
}

sub:pubinfo {
  this: dc:created "2020-10-25T00:00:00+00:00"^^xsd:dateTime ;
    pav:createdBy <nós> .
}