News:Cellosaurus release 53 + new SPARQL/RDF functionalities

Question

[Amos Bairoch]

Cellosaurus release 52 is available on https://www.cellosaurus.org/

1) Statistics

• 165949 cell lines (122193 human, 30558 mouse, 3191 rat)
• 892 species represented
• 125918 synonyms
• 470513 cross-references to 116 resources (cell line catalogs, databases, ontologies, etc.)
• 168144 references to 29655 distinct publications (papers, patents, theses, etc.)
• 15929 web links
• 9245 human, mouse and dog cell lines with STR profiles (from 952 distinct sources)
• 2582 NCIt and 1388 ORDO (Orphanet) disease terms cited
• 857 UBERON, 278 CL and 11 PO terms cited

Since release 52 of April 2025: 2081 entries were created and 20244 entries were updated

2) Changes in the format of authors in reference records

In reference records the author's name representation has changed from the traditional bibliographic format, which lists the surname followed by initials (e.g., "Nelson-Rees W.A."), to a full-name format that spells out the given name(s) in full (e.g., "Nelson-Rees, Walter Anthony"). This change improves clarity by avoiding ambiguity between authors with the same initials.

This change resulted in the following modifications to the format of the cellosaurus_refs.txt and cellosaurus.xml/xsd` files:

In cellosaurus_refs.txt, each author is now in a separate RA line.

Thus for example:

RA   Harris N.L., Gang D.L., Quay S.C., Poppema S., Zamecnik P.C.,
RA   Nelson-Rees W.A., O'Brien S.J.;

is now:

RA   Harris, Nancy Lee
RA   Gang, David L.
RA   Quay, Steven C.
RA   Poppema, Sibrandes
RA   Zamecnik, Paul Charles
RA   Nelson-Rees, Walter Anthony
RA   O'Brien, Stephen James

For the cellosaurus.xml file, the format of the "person" element was changed, as descrived in cellosaurus.xsd from:

<xs:element name="person">
      <xs:annotation>
         <xs:documentation>Describes a person.</xs:documentation>
      </xs:annotation>
      <xs:complexType>
         <xs:attribute name="name" type="xs:string" use="required"/>
      </xs:complexType>
   </xs:element>

To:

   <xs:element name="person">
      <xs:annotation>
         <xs:documentation>Describes a person.</xs:documentation>
      </xs:annotation>
      <xs:complexType>
         <xs:attribute name="name" type="xs:string" use="required"/>
         <xs:attribute name="last-name" type="xs:string" use="required"/>
         <xs:attribute name="first-names" type="xs:string" use="required"/>
         <xs:attribute name="name-suffix" type="xs:string" use="optional"/>
      </xs:complexType>
   </xs:element>

3) Changes in the DR lines

3a) Change in the abbreviation of a cross-reference

Because the PerkinElmer life sciences and diagnostics businesses have been incorportated in a new company called Revvity, the cross-references to "PerkinElmer" are now indicated as "Revvity/PerkinElmer".

Example:
DR   PerkinElmer; ES-000-A28
Is now:
DR   Revvity/PerkinElmer; ES-000-A28

4) SPARQL/RDF support

Cellosaurus is now available in RDF format, with a triple store that supports SPARQL queries

More specifically we now offer from the Tool - API submenu 6 new options:

1. SPARQL Editor (https://api.cellosaurus.org/sparql-editor). The SPARQL Editor is a tool designed to assist users in developing their SPARQL queries.
2. SPARQL Service (https://api.cellosaurus.org/sparql-service). The SPARQL service is the web service that accepts SPARQL queries over HTTP and returns results from the RDF dataset.
3. Cellosaurs Ontology (https://api.cellosaurus.org/rdf-ontology). An RDF ontology is a formal, structured representation of knowledge. It explicitly defines domain-specific concepts - such as classes and properties - enabling data to be described with meaningful semantics that both humans and machines can interpret. The Cellosaurus ontology is expressed in OWL.
4. Cellosaurus Concept Hopper (https://api.cellosaurus.org/rdf-concept-hopper). The Concept Hopper, is a tool that provides an alternative view of the Cellosaurus ontology. It focuses on a single concept at a time - either a class or a property - and shows how that concept is linked to others within the ontology, as well as how it appears in the data.
5. Cellosaurus dereferencing service (https://api.cellosaurus.org/rdf-dereferencing). The RDF dereferencing service is the mechanism that, given a URI, returns an RDF description of the resource identified by that URI, enabling clients to retrievestructured, machine-readable data about the resource from the web in different formats.
6. Cellosaurus RDF files download (https://api.cellosaurus.org/rdf-downloads). This allows you to download the Cellosaurus RDF files in Turtle (ttl) format.