Difference between revisions of "WebSchemas/BioDatabases"

From W3C Wiki
Jump to: navigation, search
m (Example Markup)
m (BiologicalDatabase)
Line 100: Line 100:
 
|}
 
|}
  
~~
 
 
== Example Markup ==
 
== Example Markup ==
 
* You can test the following examples with [http://foolip.org/microdatajs/live/ Live Microdata].
 
* You can test the following examples with [http://foolip.org/microdatajs/live/ Live Microdata].

Revision as of 07:54, 26 November 2012


This is a WebSchemas proposal Biological Databases for schema.org. See Proposals listing for more. Status: Proposal



Overview

This page discusses a schema extension for describing biological databases, proposed by MORITA Mizuki (NIBIO) on behalf of Sagace (a biological database search engine) and NBDC (National Bioscience Database Center, Japan).

Vocabulary

  • Adds a class 'BiologicalDatabaseEntry' as a kind of CreativeWork, introducing 'entryID', 'isEntryOf', 'taxonID' (or 'taxon'), 'seeAlso'. Adds 'BiologicalDatabase' also subclass of CreativeWork, with no special properties. Both also use 'breadcrumb' from WebPage.

BiologicalDatabaseEntry

Properties for a biological database:

Property Expected Type Description
Properties from Thing
additionalType (added) URL An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax.
description Text A short description of the entry.
image URL URL of an image of the entry.
name Text The name of the entry.
url URL URL of the entry.
Properties from CreativeWork
alternativeHeadline Text A secondary title of the entry.
inLanguage Language The language of the content. Please use one of the language codes from the IETF BCP 47 standard.
dateCreated Date The date on which the content was created (in ISO 8601 date format).
dateModified Date The date on which the content was most recently modified (in ISO 8601 date format).
keywords Text The keywords/tags used to describe this content.
provider Person or Organization Specifies the person or organization that distributed the content.
Properties from WebPage
breadcrumb Text A set of links that can help a user understand and navigate a website hierarchy.
relatedLink (or “seeAlso”) URL A link related to this web page, for example to other related web pages.
Original properties in BiologicalDatabaseEntry
entryID Text The identifier of the entry.
isEntryOf BiologicalDatabase Indicates the database to which the entry belongs.
taxonID (or “taxon”) Text The taxonomy identifier of the entry. Please use the NCBI Taxonomy ID.
taxon (or “taxonID”) BiologicalDatabaseEntry (or Text) The taxonomy information of the entry.
seeAlso (or “relatedLink”) BiologicalDatabaseEntry (or URL) Reference to another resource.

BiologicalDatabase

Properties for a biological database entry:

Property Expected Type Description
Properties from Thing
additionalType (added) URL An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax.
description Text A short description of the entry.
image URL URL of an image of the entry.
name Text The name of the entry.
url URL URL of the entry.
Properties from CreativeWork
alternativeHeadline Text A secondary title of the entry.
inLanguage Language The language of the content. Please use one of the language codes from the IETF BCP 47 standard.
dateCreated Date The date on which the content was created (in ISO 8601 date format).
dateModified Date The date on which the content was most recently modified (in ISO 8601 date format).
keywords Text The keywords/tags used to describe this content.
provider Person or Organization Specifies the person or organization that distributed the content.
Properties from WebPage
breadcrumb Text A set of links that can help a user understand and navigate a website hierarchy.

Example Markup

BiologicalDatabaseEntry

  1. <div itemscope itemtype="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://cellbank.nibio.go.jp/celldata/jcrb0225.htm">
  3.   <span itemprop="entryID">JCRB0225</span> [<span itemprop="name">COLO320 DM</span>]
  4.  </a></h1>
  5.  Profile: <span itemprop="description">Human colon carcinoma cell line with double minute chromosomes.</span>
  6.  Tags: <span itemprop="keywords">tumor</span>, <span itemprop="keywords">colon</span>, <span itemprop="keywords">adenocarcinoma</span>
  7.  Date accepted: <meta itemprop="dateCreated" content="1987-08-27">08/27/1987
  8.  Animal: human
  9.  Scientific Name: <meta itemprop="taxonID" content="9606">Homo sapiens
  10.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  11.   <a itemprop="url" href="http://cellbank.nibio.go.jp/">
  12.    <span itemprop="name">JCRB Cell Bank</span>
  13.   </a>
  14.  </span>
  15. </div>

BiologicalDatabase

  1. <div itemscope itemtype="http://schema.org/BiologicalDatabase">
  2.  <span itemprop="name"><a itemprop="url" href="http://cellbank.nibio.go.jp/">JCRB Cell Bank</a></span>
  3.  Profile: <span itemprop="description">JCRB Cell Bank is the first cell bank in Japan. We collect ...</span>
  4.  Date established: <meta itemprop="dateCreated" content="1984-10">10/1984
  5.  Last modified: <meta itemprop="dateModified" content="2011-02-28">02/28/2011
  6.  Operated by: <span itemprop="provider" itemscope itemtype="http://schema.org/Organization">
  7.   <a itemprop="url" href="http://www.nibio.go.jp/"><span itemprop="name">National Institute of Biomedical Innovation (NIBIO)</span></a>
  8.  </span>
  9. </div>

Your review and comments are needed!

1.How to markup taxonomy (3 candidates)

1-1. Original [use taxonID]

  1. <div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2">
  3.   <span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
  4.  </a></h1>
  5.  
  6.  Organism: <a href="http://www.uniprot.org/taxonomy/9606">Homo sapiens (human)</a>
  7.  Taxonomy ID: <a href="http://www.uniprot.org/taxonomy/9606"><span itemprop="taxonID">9606</span></a> [<a href="http://purl.uniprot.org/taxonomy/">UniProt Taxonomy</a>]
  8.  
  9.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  10.  Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
  11.  </span>
  12. </div>

1-2. Proposed change 1 [taxonID -> taxon]

  1. <div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2">
  3.   <span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
  4.  </a></h1>
  5.  
  6.  <span itemprop="taxon" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry">
  7.  Organism: <span itemprop="name">Homo sapiens</span> (human)
  8.  Taxonomy ID: <a itemprop="url" href="http://www.uniprot.org/taxonomy/9606"><span itemprop="entryID">9606</span></a> [<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase"><a itemprop="url" href="http://purl.uniprot.org/taxonomy/"><span itemprop="name">UniProt Taxonomy</span></a></span>]
  9.  </span>
  10.  
  11.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  12.  Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
  13.  </span>
  14. </div>

1-3. Proposed change 2 [taxonID -> taxon] (simpler but less useful for search engines?)

  1. <div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2">
  3.   <span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
  4.  </a></h1>
  5.  
  6.  Organism: <span itemprop="taxon">Homo sapiens</span> (human)
  7.  Taxonomy ID: <a href="http://www.uniprot.org/taxonomy/9606">9606</a> [<a href="http://purl.uniprot.org/taxonomy/">UniProt Taxonomy</a>]
  8.  
  9.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  10.  Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
  11.  </span>
  12. </div>

1-4. Or other possibilities welcome.

2. Example markup with “seeAlso” (or “relatedLink”) property (2 candidates)

2-1. Candidate 1 (“relatedLink” is NOT applicable, which cannot take ‘BiologicalDatabaseEntry’ as datatype)

  1. <div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2">
  3.   <span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
  4.  </a></h1>
  5.  
  6.  Cross-references:
  7.   KEGG: <span itemprop="seeAlso" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><a itemprop="url" href="http://purl.uniprot.org/kegg/hsa:353174"><span itemprop="name">hsa:353174</span></a></span>
  8.   RefSeq: <span itemprop="seeAlso" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><a itemprop="url" href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=NP_851321.2"><span itemprop="name">NP_851321.2</span></a></span>, <span itemprop="seeAlso" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><a itemprop="url" href="http://www.ncbi.nlm.nih.gov/nuccore/NM_180990.3"><span itemprop="name">NM_180990.3</span></a></span>
  9.   H-InvDB: <span itemprop="seeAlso" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><a itemprop="url" href="http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0027141"><span itemprop="name">HIX0027141</span></a></span>
  10.  
  11.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  12.  Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
  13.  </span>
  14. </div>

2-2. Candidate 2 (simpler but less useful for search engines?) (“relatedLink” is applicable)

  1. <div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry">
  2.  <h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2">
  3.   <span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
  4.  </a></h1>
  5.  
  6.  Cross-references:
  7.   KEGG: <a itemprop="seeAlso" href="http://purl.uniprot.org/kegg/hsa:353174">hsa:353174</a>
  8.   RefSeq: <a itemprop="seeAlso" href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=NP_851321.2">NP_851321.2</a>, <a itemprop="seeAlso" href="http://www.ncbi.nlm.nih.gov/nuccore/NM_180990.3">NM_180990.3</a>
  9.   H-InvDB: <a itemprop="seeAlso" href="http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0027141">HIX0027141</a>
  10.  
  11.  <span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">
  12.  Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
  13.  </span>
  14. </div>

2-3. Or other possibilities welcome.

Comments and Discussion

1. A Comment from Dan Brickley (2012-03-13).

  • Others have also mentioned interest in adding some notion of species.

2. Discussion in the BioHackathon ML (from 2012-08-10).

3. BioHackathon 2012 (2012-09-02/2012-09-07)

How to Join the Discussion

Please give your comments on the proposed schema by the following ways:

1. Reply to the original post on Mailing List (public-vocabs@w3.org)

2. Reply to the original post (@keyboardrobot) on Twitter

3. Reply to the original post (@keyboardrobot) on Twitter [in Japanese]

References

Search engines in the life science field

Meta data for biological databases

Validator for microdata