The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.

Prefix

ms

Preferred Prefix

MS

Keywords

obo ontology

Version

4.1.207

License

CC-BY-3.0

Links

Homepage Repository OBO OWL

Contact

Joshua Klein   0000-0003-1279-6838   mobiusklein

Pattern for Local Unique Identifiers

Local identifiers in Mass spectrometry ontology should match this regular expression:
^\d{7}$

Example Local Unique Identifier

1000560   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Mass spectrometry ontology should match this regular expression:
^MS:\d{7}$

Example CURIE

MS:1000560

MIRIAM Namespace Embedded in LUI

The legacy MIRIAM standard for generating CURIEs with this resource annotates the namespaceEmbeddedInLUI as true. This means that you may see local unique identifiers that include a redundant prefix and delimiter (also known as a banana) and therefore look like a CURIE. For , the banana looks like MS:. Therefore, you may see local unique identifiers for this resource that look like MS:1000560 (instead of the canonical form 1000560) and CURIEs for this resource that look like MS:MS:1000560 (instead of the canonical form MS:1000560). The Semantic Farm will automatically strip off the banana when standardizing local unique identifiers and CURIEs.

Publications

2013 The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

A summary of the relations in the Semantic Farm schema can be found here.

Depends On (2) (bioregistry.schema:0000017 )

PATO UO

In Collection

NFDI4Chem Collection

The metaregistry provides mappings between the Semantic Farm and other registries. There are 9 mappings to external registries for this resource with 2 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://purl.obolibrary.org/obo/MS_$1

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 1000560 is used to demonstrate the providers available for Mass spectrometry ontology. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.