EMBRACE Data and Methods Ontology
Names
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EMBRACE Data and Methods Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
EDAM
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
EDAM - Bioscientific data analysis ontology
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
Names
More detailed information about this field from each metasource.
EMBRACE Data and Methods Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
EDAM
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
EDAM - Bioscientific data analysis ontology
metasource: Biontology / Bioportalversion: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
Other names: EDAM, EDAM - Bioscientific data analysis ontology
Names
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EMBRACE Data and Methods Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
EDAM
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
EDAM - Bioscientific data analysis ontology
metasource: Biontology / Bioportalversion: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
EDAM (originally from “EMBRACE Data and Methods”) is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics.
Description
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EDAM (originally from “EMBRACE Data and Methods”) is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics.
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management. EDAM includes topics, operations, types of data and data identifiers, and data formats, relevant in data analysis and management in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use. 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 bioscientific data.
metasource: Biontology / Bioportalversion: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
Webpage:
http://edamontology.orgWebpage
More detailed information about this field from each metasource.
http://edamontology.org
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
Licence:
Name: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)Licence name
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Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
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https://creativecommons.org/licenses/by-sa/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
PMID: 23479348
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
https://doi.org/10.7490/f1000research.1118900.1
metasource: Biontology / Bioportal
version: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
Publications
More detailed information about this field from each metasource.
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
PMID: 23479348
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
https://doi.org/10.7490/f1000research.1118900.1
metasource: Biontology / Bioportalversion: unstable(1.26_dev) extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/EDAM
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EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
PubMed citations: 73.
73 articles citing: EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. PMID:35879672
A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks. PMID:35715466
BD2K Training Coordinating Center's ERuDIte: the Educational Resource Discovery Index for Data Science. PMID:35548703
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
Integrated Genome Browser App Store. PMID:35179566
Improving bioinformatics software quality through incorporation of software engineering practices. PMID:35111923
Expression atlas of avian neural crest proteins: Neurulation to migration. PMID:34990731
Perspectives on automated composition of workflows in the life sciences. PMID:34804501
Design considerations for workflow management systems use in production genomics research and the clinic. PMID:34737383
Simplifying the development of portable, scalable, and reproducible workflows. PMID:34643507
The role of metadata in reproducible computational research. PMID:34553169
Bioimage analysis workflows: community resources to navigate through a complex ecosystem. PMID:34136134
Aviator: a web service for monitoring the availability of web services. PMID:34038559
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. PMID:33849055
Fantastic databases and where to find them: Web applications for researchers in a rush. PMID:33821874
APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry. PMID:33720735
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
biotoolsSchema: a formalized schema for bioinformatics software description. PMID:33506265
Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites. PMID:33319904
Ten simple rules for making training materials FAIR. PMID:32437350
TeSS: a platform for discovering life-science training opportunities. PMID:32044952
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. PMID:31960040
JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools. PMID:31913853
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. PMID:31675414
Community curation of bioinformatics software and data resources. PMID:31624831
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. PMID:31506435
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. PMID:31504201
The bio.tools registry of software tools and data resources for the life sciences. PMID:31405382
BioShake: a Haskell EDSL for bioinformatics workflows. PMID:31328031
Software engineering for scientific big data analysis. PMID:31121028
IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments. PMID:30855969
Eleven quick tips to build a usable REST API for life sciences. PMID:30543619
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. PMID:30521012
Automated workflow composition in mass spectrometry-based proteomics. PMID:30060113
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Community-Driven Data Analysis Training for Biology. PMID:29953864
SciApps: a cloud-based platform for reproducible bioinformatics workflows. PMID:29897418
Where to search top-K biomedical ontologies? PMID:29579141
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. PMID:29390967
Using bio.tools to generate and annotate workbench tool descriptions. PMID:29333231
COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies. PMID:29083911
An architecture for genomics analysis in a clinical setting using Galaxy and Docker. PMID:29048555
Dietary and health biomarkers-time for an update. PMID:28974991
Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. PMID:28694792
ReGaTE: Registration of Galaxy Tools in Elixir. PMID:28402416
From the evaluation of existing solutions to an all-inclusive package for biobanks. PMID:28344915
Bio-TDS: bioscience query tool discovery system. PMID:27924016
EuPathDB: the eukaryotic pathogen genomics database resource. PMID:27903906
Text mining resources for the life sciences. PMID:27888231
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE. PMID:27751176
Top 10 metrics for life science software good practices. PMID:27635232
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. PMID:27433158
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability. PMID:27309738
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. PMID:27137889
The 2015 Bioinformatics Open Source Conference (BOSC 2015). PMID:26914653
BioShaDock: a community driven bioinformatics shared Docker-based tools registry. PMID:26913191
Tools and data services registry: a community effort to document bioinformatics resources. PMID:26538599
Challenges and Opportunities for Exploring Patient-Level Data. PMID:26504779
Use of semantic workflows to enhance transparency and reproducibility in clinical omics. PMID:26289940
Ontology application and use at the ENCODE DCC. PMID:25776021
Community-driven development for computational biology at Sprints, Hackathons and Codefests. PMID:25472764
Structuring research methods and data with the research object model: genomics workflows as a case study. PMID:25276335
BioSWR--semantic web services registry for bioinformatics. PMID:25233118
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. PMID:24564249
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517 - https://doi.org/10.7490/f1000research.1118900.1
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data acquisition
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data transformation
metasource: Fairsharing.org
version: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
data acquisition
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data transformation
metasource: Fairsharing.orgversion: FAIRsharing.org: EDAM; EMBRACE Data and Methods Ontology; DOI: https://doi.org/10.25504/FAIRsharing.a6r7zs; Last edited: Jan. 5, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data acquisition data transformation
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