WebSchemas/BioDatabases
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== Example Markup == | == Example Markup == | ||
Revision as of 08:17, 26 November 2012
This is a WebSchemas proposal Biological Databases for schema.org. See Proposals listing for more. Status: Proposal
Contents |
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
- You can test the following examples with Live Microdata.
- Please see the Sagace schema page for more examples.
BiologicalDatabaseEntry
<div itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://cellbank.nibio.go.jp/celldata/jcrb0225.htm"><span itemprop="entryID">JCRB0225</span> [<span itemprop="name">COLO320 DM</span>]
</a></h1>Profile: <span itemprop="description">Human colon carcinoma cell line with double minute chromosomes.</span>
Tags: <span itemprop="keywords">tumor</span>, <span itemprop="keywords">colon</span>, <span itemprop="keywords">adenocarcinoma</span>
Date accepted: <meta itemprop="dateCreated" content="1987-08-27">08/27/1987Animal: human
Scientific Name: <meta itemprop="taxonID" content="9606">Homo sapiens<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase"><a itemprop="url" href="http://cellbank.nibio.go.jp/"><span itemprop="name">JCRB Cell Bank</span>
</a></span></div>
BiologicalDatabase
<div itemscope itemtype="http://schema.org/BiologicalDatabase"><span itemprop="name"><a itemprop="url" href="http://cellbank.nibio.go.jp/">JCRB Cell Bank</a></span>
Profile: <span itemprop="description">JCRB Cell Bank is the first cell bank in Japan. We collect ...</span>
Date established: <meta itemprop="dateCreated" content="1984-10">10/1984Last modified: <meta itemprop="dateModified" content="2011-02-28">02/28/2011Operated by: <span itemprop="provider" itemscope itemtype="http://schema.org/Organization"><a itemprop="url" href="http://www.nibio.go.jp/"><span itemprop="name">National Institute of Biomedical Innovation (NIBIO)</span></a>
</span></div>
Your review and comments are needed!
- You can test the following examples with Live Microdata.
1.How to markup taxonomy (3 candidates)
1-1. Original [use taxonID]
<div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2"><span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
</a></h1>Organism: <a href="http://www.uniprot.org/taxonomy/9606">Homo sapiens (human)</a>
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>]
<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
</span></div>
1-2. Proposed change 1 [taxonID -> taxon]
<div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2"><span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
</a></h1><span itemprop="taxon" itemscope itemtype="http://schema.org/BiologicalDatabaseEntry">Organism: <span itemprop="name">Homo sapiens</span> (human)
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>]
</span><span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
</span></div>
1-3. Proposed change 2 [taxonID -> taxon] (simpler but less useful for search engines?)
<div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2"><span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
</a></h1>Organism: <span itemprop="taxon">Homo sapiens</span> (human)
Taxonomy ID: <a href="http://www.uniprot.org/taxonomy/9606">9606</a> [<a href="http://purl.uniprot.org/taxonomy/">UniProt Taxonomy</a>]
<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
</span></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)
<div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2"><span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
</a></h1>Cross-references:
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>
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>
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>
<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
</span></div>
2-2. Candidate 2 (simpler but less useful for search engines?) (“relatedLink” is applicable)
<div itemscope itemtype ="http://schema.org/BiologicalDatabaseEntry"><h1><a itemprop="url" href="http://www.uniprot.org/uniprot/Q401N2"><span itemprop="entryID">Q401N2</span> [<span itemprop="name">Zinc-activated ligand-gated ion channel</span>]
</a></h1>Cross-references:
KEGG: <a itemprop="seeAlso" href="http://purl.uniprot.org/kegg/hsa:353174">hsa:353174</a>
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>
H-InvDB: <a itemprop="seeAlso" href="http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0027141">HIX0027141</a>
<span itemprop="isEntryOf" itemscope itemtype="http://schema.org/BiologicalDatabase">Database: <a itemprop="url" href="http://www.uniprot.org/"><span itemprop="name">UniProt</span></a>
</span></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).
- https://groups.google.com/forum/#!topic/biohackathon/8y73xtWSHxc%5B1-25%5D
- Taxonomy ID - Simplicity or Flexibility? (Jerven Bolleman)
3. BioHackathon 2012 (2012-09-02/2012-09-07)
- https://github.com/dbcls/bh12/wiki/Schema.org-extension/
- We discussed with the “Standard RDF representation for glycans” group.
- How to mark up trivial name (e.g., sialyl-lewis-x, lactosamine)
- sameAs, seeAlso or relatedLink
- taxonID or taxon
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
- Entrez (NCBI) -- http://www.ncbi.nlm.nih.gov/sites/gquery
- EB-eye (EBI) -- http://www.ebi.ac.uk/ebisearch/
- Life Science Database Cross Search (NBDC) -- http://biosciencedbc.jp/dbsearch/en/
- Sagace (NIBIO) -- http://sagace.nibio.go.jp/en/
Meta data for biological databases
- BioDBcore -- http://biodbcore.org/
- Catalogue of DBs with BioDBcore -- http://biosharing.org/biodbcore
Validator for microdata
- You can test the above example markups with Live Microdata.
