BioProject and BioSample notes

Reading BioProject XML files

<bioproject class="XMLReader">
  <sourcePath>...</sourcePath>
  <xslTransform>res://XMLReader/bioproject2alvisnlp.xslt</xslTransform> <!-- since alvisnlp commit 363df429a80b960febfb5022182b9d2743e4398b -->
</bioproject>

• Documents
  • @id : BioProject accession number
  • @archive : database (NCBI, EBI, etc)
• Sections
  • Name : project name
  • Title : project title
  • Description : project description
  • Organism : project target organism
    • @name : organism name (with strain name if given)
    • @taxid : NCBI taxonomy identifier Not sure the strain taxid is given, might be the species or subspecies
    • Layer taxa spanning the whole section, with @taxid
    • The organism is not always recorded, might need to search in other sections

Reading BioSample XML files

<bioproject class="XMLReader">
  <sourcePath>...</sourcePath>
  <xslTransform>res://XMLReader/biosample2alvisnlp.xslt</xslTransform> <!-- since alvisnlp commit 363df429a80b960febfb5022182b9d2743e4398b -->
</bioproject>

• Documents
  • @id : BioSample accession number
  • Sections
    • Title : sample title
    • Paragraph : comments (maybe none or several)
    • Organism : project target organism
      • @name : organism name (with strain name if given)
      • @taxid : NCBI taxonomy identifier Not sure the strain taxid is given, might be the species or subspecies
      • Layer taxa spanning the whole section, with @taxid
      • The organism is not always recorded, might need to search in other sections
    • isolation_source : isolation source attribute, not always recorded, might be present in other sections
    • host : host attribute
    • sample type : sample type attribute
    • geo_loc_name : geographical location attribute
    • altitude : altitude attribute
    • lat_lon : latitude-longitude coordinates attribute