Repository details

OrthoMCL

Name of repository
OrthoMCL
Additional name(s)
  • Ortholog Groups of Protein Sequences
Repository URL
https://orthomcl.org/orthomcl/app
Subject(s)
Description
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.
Contact
Content type(s)
Keyword(s)
Persistent identifier(s) of the repository
  • RRID:SCR_007839
  • RRID:nif-0000-03230
  • FAIRsharing_doi:10.25504/FAIRsharing.283caf
Repository size
832 organisms (682 Peripheral and 150 Core organisms)
Repository type(s)
  • disciplinary
Mission statement for designated community
https://orthomcl.org/orthomcl/app/static-content/OrthoMCL/about.html
Research data repository language(s)
  • English
Data and/or service provider
  • data provider
Institution name
National Institutes of Health, National Institute of Allergy and Infectious Diseseases, Department of Health and Human Services
Additional name(s)
  • NIAID
Country
United States
Type(s) of responsibility
  • funding
Type of institution
non-profit
Institution name
University of Pennsylvania, Penn Institute for Biomedical Informatics
Country
United States
Type(s) of responsibility
  • general
Type of institution
non-profit

Policies (1)

Policy Name
Data Access Policy

Database access

Type of access to research data repository
open

Data access (1)

Type of access to data
open

Data licenses (2)

DataLicense
other
DataLicense
other

Data upload (1)

Type of data upload
restricted
Data upload restriction type(s)
  • other

Data upload license (1)

Data upload license name
Data Submission Policy
Name of the repository software
  • CKAN
Versioning
yes
Data citation guideline
https://veupathdb.org/veupathdb/app/static-content/about.html#about_citing
Enhanced Publication
unknown
Quality management
unknown

Application programming interfaces (2)

API type
REST
API type
REST

Metadata standards (1)

Metadata standard name
Repository-Developed Metadata Schemas
Metadata standard scheme
DCC

Remarks

Entry date
2017-09-05
Last update
2023-10-04
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Cite this re3data.org record:

re3data.org: OrthoMCL; editing status 2023-10-04; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FZ27 last accessed: 2024-04-24