EDAM - The data analysis and management ontology - Superfamily entry format - Classes

EDAM - The data analysis and management ontology

Last uploaded: February 26, 2021

Details

Acronym	EDAM
Visibility	Public
Description	EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. As a reference article (citation), please use https://doi.org/10.7490/f1000research.1118900.1
Status	Production
Format	OWL
Contact	GitHub repository, https://github.com/edamontology/edamontology Hervé Ménager, herve.menager@pasteur.fr Matúš Kalaš, drmatuskalas@duck.com
Categories	All Organisms, Biomedical Resources, Genomic and Proteomic, Other, Vocabularies

Version	Released	Uploaded	Downloads
1.25-20240924T0027Z-unstable(1.26) (Parsed, Indexed, Metrics, Annotator)	09/24/2024	02/26/2021	OWL \| CSV \| RDF/XML \| Diff
1.25 (Archived)	06/18/2020	06/18/2020	OWL \| Diff
1.24 (Archived)	01/16/2020	01/16/2020	OWL
1.24-PRERELEASE (Archived)	01/14/2020	01/14/2020	OWL
1.23 (Archived)	07/16/2019	07/16/2019	OWL \| Diff
1.22 (Archived)	05/14/2019	05/12/2019	OWL \| Diff
1.21 (Archived)	07/31/2018	07/30/2018	OWL \| Diff
1.20 (Archived)	12/31/2017	12/15/2017	OWL \| Diff
1.19 (Archived)	10/31/2017	10/30/2017	OWL \| Diff
1.18 (Archived)	07/04/2017	07/06/2017	OWL \| Diff
1.17 (Archived)	04/27/2017	04/28/2017	OWL \| Diff
1.16 (Archived)	10/31/2016	11/01/2016	OWL \| Diff
1.15 (Archived)	05/16/2016	05/16/2016	OWL \| Diff
1.14 (Archived)	02/26/2016	02/26/2016	OWL \| Diff
1.13 (Archived)	02/09/2016	02/08/2016	OWL \| Diff
1.12 (Archived)	12/18/2015	01/06/2016	OWL \| Diff
1.11 (Archived)	07/09/2015	07/09/2015	OWL \| Diff
1.10 (Archived)	07/03/2015	07/03/2015	OWL \| Diff
1.10 (Archived)	07/03/2015	07/03/2015	OWL \| Diff
1.9 (Archived)	02/02/2015	02/02/2015	OWL \| Diff
1.8 (Archived)	12/16/2014	12/16/2014	OWL \| Diff
1.7 (Archived)	12/08/2014	12/08/2014	OWL \| Diff
1.6 (Archived)	11/18/2014	11/18/2014	OWL \| Diff
1.5 (Archived)	11/14/2014	11/14/2014	OWL \| Diff
1.4 (Archived)	10/06/2014	09/26/2014	OWL \| Diff
1.3 (Archived)	02/20/2014	02/18/2014	OWL \| Diff
1.2 (Archived)	12/14/2012	12/14/2012	OWL \| Diff
1.1 (Archived)	07/05/2012	12/10/2012	OBO \| Diff
1 (Archived)	01/13/2012	01/20/2012	OBO
Beta13 (Archived)	12/05/2011	12/05/2011	OBO
beta12 (Archived)	06/17/2011	06/17/2011	OBO
beta11 (Archived)	01/22/2011	01/22/2011	OBO
beta10 (Archived)	07/10/2010	12/01/2010	OBO
beta09 (Archived)	07/10/2010	10/07/2010	OBO
beta08 (Archived)	05/28/2010	08/18/2010	OBO
beta07 (Archived)	05/28/2010	05/28/2010	OBO
beta05 (Archived)	06/11/2010	05/14/2010	OBO
more...

Biomedical Topics Ontology: An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM.
EDAM Topics Subset: An ontology of bioinformatics, biological and biomedical topics (EDAM Topics)

Classes	3,511
Individuals	3
Properties	13
Maximum depth	8
Maximum number of children	1,119
Average number of children	7
Classes with a single child	163
Classes with more than 25 children	15
Classes with no definition	1

CEDAR FAIR Funder Form

Common Workflow Language

Computational Biology Institute of Montpellier

Id	http://edamontology.org/format_1578 http://edamontology.org/format_1578
Preferred Name	Superfamily entry format
Definitions	Entry format for the Superfamily protein secondary database.
Obsolete	true
Type	http://www.w3.org/2002/07/owl#Class

label	Superfamily entry format
prefLabel	Superfamily entry format
inSubset	http://edamontology.org/obsolete
consider	http://edamontology.org/format_2331
prefixIRI	format_1578
subClassOf	http://www.w3.org/2002/07/owl#DeprecatedClass
hasDefinition	Entry format for the Superfamily protein secondary database.
deprecated	true
type	http://www.w3.org/2002/07/owl#Class
Obsolete since	beta12orEarlier
Old parent	http://www.w3.org/2002/07/owl#Thing
Created in	March 12, 2025

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Subject	Author	Type	Class	Created
Other disease analysis?	mkalas	Comment	http://edamontology.org/operation_4033	2023-03-30
Data integration (operation)	mkalas	Comment	http://edamontology.org/operation_3453	2022-05-13
Add broad synonym FAIR research outputs?	mkalas	Comment	http://edamontology.org/topic_4012	2022-05-04
Rename to "Sex or gender differences in"..."(human) health/disease/medicine"	mkalas	Comment	http://edamontology.org/topic_3410	2022-01-20
Genome accession vs. identifier vs. build identifier	mkalas	Comment	http://edamontology.org/data_2749	2021-12-15
Together with Transcriptomics, Gene expression study/analysis, EWAS, ...	mkalas	Comment	http://edamontology.org/topic_3517	2021-11-29
Do we also need Gene imprinting and similar topics?	mkalas	Comment	http://edamontology.org/topic_3974	2021-11-29
Add disordered protein/region conformation assignment? And tertiary structure?	mkalas	Comment	http://edamontology.org/operation_0320	2021-11-12
Integrative bioinformatics	mkalas	Comment	http://edamontology.org/topic_0091	2021-10-07
RDF? OWL?	mkalas	Comment	http://edamontology.org/format_3156	2021-09-05
Also quaternary -> rather call 3D?	mkalas	Comment	http://edamontology.org/format_2033	2021-09-02
Add Global health etc., Prevention, Lifestyle etc., distinguish clinical & preventive, add Healthcare?	mkalas	Comment	http://edamontology.org/topic_3305	2021-08-27
Distinguish clinical & scientific?	mkalas	Comment	http://edamontology.org/topic_0804	2021-08-27
Data collection vs. acquisition	mkalas	Comment	http://edamontology.org/topic_3077	2021-08-15
New Class Proposal: Glycomics under Omics	mkalas	New Class Proposal	http://edamontology.org/topic_3292	2021-08-10
Document/Text classification	mkalas	Comment	http://edamontology.org/operation_0306	2021-07-28
Event extraction	mkalas	Comment	http://edamontology.org/operation_3625	2021-07-28
Syntactic analysis	mkalas	Comment	http://edamontology.org/operation_0306	2021-07-28
under HDF5 + add concrete NetCDF standards (e.g. CF..)	mkalas	Comment	http://edamontology.org/format_3650	2021-07-27
Add OME-Zarr	mkalas	Comment	http://edamontology.org/format_3915	2021-07-27
under TIFF	mkalas	Comment	http://edamontology.org/format_3727	2021-07-27
Visual analaysis	mkalas	Comment	http://edamontology.org/operation_0337	2021-07-26
XR, AR, VR, Mixed R visualisation	mkalas	Comment	http://edamontology.org/operation_0337	2021-07-26
Interactive visualisation	mkalas	Comment	http://edamontology.org/operation_0337	2021-07-26
Struct bio v. Struct bioinf v. Cheminf v. Biophys ...	mkalas	Comment	http://edamontology.org/topic_1317	2021-07-26
Merge with Bioinformatics	mkalas	Comment	http://edamontology.org/topic_3307	2021-07-25
Incl. Sensitive data (handling)	mkalas	Comment	http://edamontology.org/topic_3263	2021-07-25
Probably needs a couple of refined concepts	mkalas	Comment	http://edamontology.org/topic_3174	2021-07-25
Pathogens	mkalas	Comment	http://edamontology.org/topic_3324	2021-07-25
Create a generic topic Life science(s)/Biosciences	mkalas	Comment	http://edamontology.org/topic_3070	2021-07-25
Merge with computational chemistry?	mkalas	Comment	http://edamontology.org/topic_2258	2021-07-25
Refine	mkalas	Comment	http://edamontology.org/topic_3305	2021-07-25
Refactor Env science(s)	mkalas	Comment	http://edamontology.org/topic_3855	2021-07-25
Chem(o)informatics synonym	mkalas	Comment	http://edamontology.org/topic_3332	2021-07-25
Geoscience(s) & Astronomy/Astroscience(s)	mkalas	Comment	http://edamontology.org/topic_3318	2021-07-25
Merge with (Bio)Medical science(s)?	mkalas	Comment	http://edamontology.org/topic_3303	2021-07-25
More RDF formats?	mkalas	Comment	http://edamontology.org/format_2376	2021-07-20
Confusing OWL vs RDF	mkalas	Comment	http://edamontology.org/format_2197	2021-07-20
ttl extension?	mkalas	Comment	http://edamontology.org/format_3255	2021-07-20
Unmix with historical concepts [Old bug found:(]	mkalas	Comment	http://edamontology.org/topic_4011	2021-07-20
(SKOS not needed?)	mkalas	Comment	http://edamontology.org/format_2197	2021-07-20
Topics to add and to leave out(?)	mkalas	Comment	http://edamontology.org/topic_4010	2021-07-13
Data rescue	mkalas	Comment	http://edamontology.org/topic_4011	2021-07-13
New Class Proposal: Missing concept(s)	mkalas	New Class Proposal	http://edamontology.org/topic_0003	2021-07-13
Add main missing ecology topics	mkalas	Comment	http://edamontology.org/topic_0610	2021-07-13
Optical (genome) mapping	mkalas	Comment	http://edamontology.org/topic_3382	2021-07-07
To be updated from EDAM Bioimaging	mkalas	Comment	http://edamontology.org/operation_3443	2021-07-06
To be updated from EDAM Bioimaging	mkalas	Comment	http://edamontology.org/topic_3474	2021-07-06
To be updated from EDAM Bioimaging	mkalas	Comment	http://edamontology.org/topic_3382	2021-07-06
(Molecular) contact map alignment	mkalas	Comment	http://edamontology.org/data_1479	2021-06-12

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