Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling.
compatibility
composability
modularity
process description
quality verification
reusability
systems biology
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
02 09 2021
02 09 2021
Historique:
received:
20
01
2021
revised:
05
03
2021
accepted:
08
03
2021
pubmed:
10
4
2021
medline:
23
11
2021
entrez:
9
4
2021
Statut:
ppublish
Résumé
Detailed maps of the molecular basis of the disease are powerful tools for interpreting data and building predictive models. Modularity and composability are considered necessary network features for large-scale collaborative efforts to build comprehensive molecular descriptions of disease mechanisms. An effective way to create and manage large systems is to compose multiple subsystems. Composable network components could effectively harness the contributions of many individuals and enable teams to seamlessly assemble many individual components into comprehensive maps. We examine manually built versions of the RAS-RAF-MEK-ERK cascade from the Atlas of Cancer Signalling Network, PANTHER and Reactome databases and review them in terms of their reusability and composability for assembling new disease models. We identify design principles for managing complex systems that could make it easier for investigators to share and reuse network components. We demonstrate the main challenges including incompatible levels of detail and ambiguous representation of complexes and highlight the need to address these challenges.
Identifiants
pubmed: 33834185
pii: 6217719
doi: 10.1093/bib/bbab103
pmc: PMC8425390
pii:
doi:
Substances chimiques
raf Kinases
EC 2.7.11.1
ras Proteins
EC 3.6.5.2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM119771
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press.
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