WebSchemas/BioDatabases

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

1 Overview
2 Vocabulary
- 2.1 BiologicalDatabaseEntry
- 2.2 BiologicalDatabase
3 Example Markup
- 3.1 BiologicalDatabaseEntry
- 3.2 BiologicalDatabase
4 Your review and comments are needed!
- 4.1 1.How to markup taxonomy (3 candidates)
- 4.2 2. Example markup with “seeAlso” (or “relatedLink”) property (2 candidates)
5 Comments and Discussion
6 How to Join the Discussion
7 References

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">08/27/1987

```
 Animal: 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">10/1984

 Last modified: <meta itemprop="dateModified" content="2011-02-28">02/28/2011

 Operated 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.

WebSchemas/BioDatabases

From W3C Wiki

Contents

Overview

Vocabulary

BiologicalDatabaseEntry

BiologicalDatabase

Example Markup

BiologicalDatabaseEntry

BiologicalDatabase

Your review and comments are needed!

1.How to markup taxonomy (3 candidates)

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

Comments and Discussion

How to Join the Discussion

References

Search engines in the life science field

Meta data for biological databases

Validator for microdata

Views

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