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Minimum Information about a Molecular Interaction Causal Statement

Abbreviation: MI2CAST

General Information

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines describe the minimum and necessary information to depict causal interactions in molecular biology, as well as contextual details. The aim is to homogenize their representation for better usability and understanding, by making the data “FAIR” (Findable, Accessible, Interoperable and Reproducible). This checklist considers terms used in different formats (e.g., PSI-MITAB2.8, BEL, GO-CAM) and covers the full range of metadata that should ideally be annotated during the curation process to enrich the description of a molecular causal interaction. Complying with these guidelines should be considered as good practice for the annotation of causal statements to generate high quality statements.

Homepage https://github.com/MI2CAST/MI2CAST

Countries that developed this resource Norway

Created in 2020

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: MI2CAST; Minimum Information about a Molecular Interaction Causal Statement; DOI: https://doi.org/10.25504/FAIRsharing.zpCPN7; Last edited: July 31, 2020, 2:06 p.m.; Last accessed: Jul 30 2021 5:07 p.m.

This record is maintained by vtoure

Record added: June 7, 2020, 10:12 a.m.
Record updated: July 12, 2020, 11 a.m. by vtoure.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.zpCPN7' by 'vtoure' at 11:00, 12 Jul 2020 (approved):

	'publications' has been modified:
		Before:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Preprints|2020
		After:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Bioinformatics|2020
		Added:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Bioinformatics|2020
		Removed:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Preprints|2020

Edits to 'https://fairsharing.org/FAIRsharing.zpCPN7' by 'vtoure' at 10:56, 10 Jun 2020 (approved):

	'organizations' has been modified:
		Before:
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Undefined
			NTNU - Norwegian University of Science and Technology|https://www.ntnu.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Undefined
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Undefined
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Undefined
			University College London, UK|http://www.ucl.ac.uk/smb|Undefined
			GSK|https://www.gsk.com/|Undefined
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Undefined
			University of Calabria|https://www.unical.it/|Undefined
			Enveda Therapeutics|https://envedatherapeutics.com/|Undefined
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Undefined
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Undefined
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Undefined
			University of Southern California (USC), USA|http://www.usc.edu|Undefined
		After:
			NTNU - Norwegian University of Science and Technology|https://www.ntnu.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Maintains
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Maintains
			University College London, UK|http://www.ucl.ac.uk/smb|Maintains
			GSK|https://www.gsk.com/|Maintains
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Maintains
			University of Calabria|https://www.unical.it/|Maintains
			Enveda Therapeutics|https://envedatherapeutics.com/|Maintains
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Maintains
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Maintains
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Maintains
			University of Southern California (USC), USA|http://www.usc.edu|Maintains
		Added:
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Maintains
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Maintains
			University College London, UK|http://www.ucl.ac.uk/smb|Maintains
			GSK|https://www.gsk.com/|Maintains
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Maintains
			University of Calabria|https://www.unical.it/|Maintains
			Enveda Therapeutics|https://envedatherapeutics.com/|Maintains
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Maintains
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Maintains
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Maintains
			University of Southern California (USC), USA|http://www.usc.edu|Maintains
		Removed:
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Undefined
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Undefined
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Undefined
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Undefined
			University College London, UK|http://www.ucl.ac.uk/smb|Undefined
			GSK|https://www.gsk.com/|Undefined
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Undefined
			University of Calabria|https://www.unical.it/|Undefined
			Enveda Therapeutics|https://envedatherapeutics.com/|Undefined
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Undefined
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Undefined
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Undefined
			University of Southern California (USC), USA|http://www.usc.edu|Undefined

Edits to 'https://fairsharing.org/FAIRsharing.zpCPN7' by 'The FAIRsharing Team' at 14:56, 09 Jun 2020 (approved):

	'organizations' has been modified:
		Before:
			NTNU - Norwegian University of Science and Technology|https://www.ntnu.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Undefined
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Undefined
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Undefined
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Undefined
			University College London, UK|http://www.ucl.ac.uk/smb|Undefined
			GSK|https://www.gsk.com/|Undefined
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Undefined
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Undefined
			University of Calabria|https://www.unical.it/|Undefined
			Enveda Therapeutics|https://envedatherapeutics.com/|Undefined
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Undefined
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Undefined
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Undefined
			University of Southern California (USC), USA|http://www.usc.edu|Undefined
		After:
			Universit d'Aix-Marseille, Marseille, France|https://www.univ-amu.fr/|Undefined
			NTNU - Norwegian University of Science and Technology|https://www.ntnu.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Undefined
			Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA|http://berkeleybop.org/|Undefined
			University of Heidelberg, Germany|http://www.uni-heidelberg.de/|Undefined
			University College London, UK|http://www.ucl.ac.uk/smb|Undefined
			GSK|https://www.gsk.com/|Undefined
			Department of Biology, University of Rome Tor Vergata, Rome, Italy|http://www.moleculargenetics.it/bcb/|Undefined
			University of Calabria|https://www.unical.it/|Undefined
			Enveda Therapeutics|https://envedatherapeutics.com/|Undefined
			Department of Medicine, University of California San Diego|https://ucsd.edu/|Undefined
			RWTH Aachen, Germany|http://www.dbis.rwth-aachen.de/|Undefined
			Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France|http://www.biologie.ens.fr/depbio/,lang=eng|Undefined
			University of Southern California (USC), USA|http://www.usc.edu|Undefined
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Undefined

	'supportLinks' has been modified:
		Before:
		After:
			forum|https://github.com/MI2CAST/MI2CAST/issues
		Added:
			forum|https://github.com/MI2CAST/MI2CAST/issues
		Removed:

	'description' has been modified:
		Before: MI2CAST guides on concepts that should be archived together with a causal interaction. This checklist considers terms used in different formats (e.g., PSI-MITAB2.8, BEL, GO-CAM) and covers the full range of metadata that should ideally be annotated during the curation process to enrich the description of a molecular causal interaction. MI2CAST checklist advises: 1) the molecular biologists to experimentally assess and describe a list of criteria, when conducting experiments, necessary to contextualize causal interactions; 2) the curators to consider and extract a list of metadata while curating causal interactions; 3) the data consumers to access persistent information and fully contextualized data to be able to select causal statements that comply with the system analysed in their case study. Complying with these guidelines should be considered as good practice for the annotation of causal statements to generate high quality statements.
		After: The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines describe the minimum and necessary information to depict causal interactions in molecular biology, as well as contextual details. The aim is to homogenize their representation for better usability and understanding, by making the data ?FAIR? (Findable, Accessible, Interoperable and Reproducible). This checklist considers terms used in different formats (e.g., PSI-MITAB2.8, BEL, GO-CAM) and covers the full range of metadata that should ideally be annotated during the curation process to enrich the description of a molecular causal interaction. Complying with these guidelines should be considered as good practice for the annotation of causal statements to generate high quality statements.

	'onto_disciplines' has been modified:
		Before:
		After:
			Systems Biology
			Systems Medicine
		Added:
			Systems Biology
			Systems Medicine
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			View / Download Guidelines
		Added:
			View / Download Guidelines
		Removed:

	'related_standards' has been modified:
		Before:
			Minimum Information about a Molecular Interaction Experiment
		After:
			Cell Ontology
			UBER anatomy ONtology
			Plant Ontology
			Chemical Entities of Biological Interest
			Sequence Ontology
			BRENDA tissue / enzyme source
			Ontology for Biomedical Investigations
			Evidence codes
			Gene Ontology
			PSI Molecular Interaction Controlled Vocabulary
			Protein MODification
			NCBI Taxonomy
			Minimum Information about a Molecular Interaction Experiment
			Fungal Gross Anatomy Ontology
			OBO Relations Ontology
			Digital Object Identifier
		Added:
			Cell Ontology
			UBER anatomy ONtology
			Plant Ontology
			Chemical Entities of Biological Interest
			Sequence Ontology
			BRENDA tissue / enzyme source
			Ontology for Biomedical Investigations
			Evidence codes
			Gene Ontology
			PSI Molecular Interaction Controlled Vocabulary
			Protein MODification
			NCBI Taxonomy
			Fungal Gross Anatomy Ontology
			OBO Relations Ontology
			Digital Object Identifier
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			molecular entity
			molecular interaction
		Added:
			molecular entity
			molecular interaction
		Removed:

	'taxonomies' has been modified:
		Before:
			Not applicable
		After:
			All
		Added:
			All
		Removed:
			Not applicable

Edits to 'https://fairsharing.org/FAIRsharing.zpCPN7' by 'vtoure' at 10:15, 07 Jun 2020 (approved):

	'publications' has been modified:
		Before:
		After:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Preprints|2020
		Added:
			The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)|Tour et al.|Preprints|2020
		Removed:

Support

General

forum

GitHub Issue Tracker

Additional Information

Contact

Vasundra Touré ORCID

Tools

causalBuilder

https://mi2cast.github.io/causalBuilder/

1.0

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Data Release

View / Download Guidelines

https://github.com/MI2CAST/MI2CAST/blob/master/docs/MI2CAST_guideline. ...

Publications

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Touré et al.
Bioinformatics 2020

Link to Publication

Related Standards

Reporting Guidelines

Minimum Information about a Molecular Interaction Experiment

Terminology Artifacts

Models and Formats

Visual Syntax Method

Identifier Schemas

Digital Object Identifier

Metrics

No metrics standards defined

Related Databases (3)

PubMed
PubMed is a search engine of biomedical literature, provided as a service of the U.S. National Library of Medicine and includes more than 25 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

SIGnaling Network Open Resource
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.

Cellosaurus
The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by vtoure

Maintains

NTNU - Norwegian University of Science and Technology (University) Lead
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)
Universit d'Aix-Marseille, Marseille, France (University)
Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute)
Berkeley BOP (BBOP), Lawrence Berkeley National Labs (LBNL), Berkeley, CA, USA (Research institute)
University of Heidelberg, Germany (University)
University College London, UK (University)
GSK (Company)
Department of Biology, University of Rome Tor Vergata, Rome, Italy (University)
University of Calabria (University)
Enveda Therapeutics (Company)
Department of Medicine, University of California San Diego (University)
RWTH Aachen, Germany (University)
Departement de Biologie (IBENS), Ecole Normale Superieure, Paris, France (Research institute)
University of Southern California (USC), USA (University)

Minimum Information about a Molecular Interaction Causal Statement

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