How to cite this record FAIRsharing.org: ECO; Evidence codes; DOI: https://doi.org/10.25504/FAIRsharing.wvpgwn; Last edited: July 5, 2019, 11:49 a.m.; Last accessed: Jul 08 2020 4:18 a.m.
Record updated: June 21, 2019, 4:52 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.wvpgwn' by 'The FAIRsharing Team' at 09:39, 12 Jun 2019 (approved): 'organizations' has been modified: Before: National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds After: National Science Foundation (NSF), USA|https://www.nsf.gov/|Funds National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds U.S. Department of Energy|http://genomicscience.energy.gov/datasharing/|Funds Added: National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds U.S. Department of Energy|http://genomicscience.energy.gov/datasharing/|Funds Removed: 'grants' has been modified: Before: 1458400 After: 1458400 DE-AC02-05CH11231 R01 GM089636 R01-HG02729- 01 U41-HG002223 U41HG008735 Added: DE-AC02-05CH11231 R01 GM089636 R01-HG02729- 01 U41-HG002223 U41HG008735 Removed: 'supportLinks' has been modified: Before: online documentation|http://obofoundry.github.io/ontology/eco.html After: help|http://www.evidenceontology.org/userguide/ online documentation|http://obofoundry.github.io/ontology/eco.html online documentation|http://www.evidenceontology.org/docs/ Added: help|http://www.evidenceontology.org/userguide/ online documentation|http://www.evidenceontology.org/docs/ Removed: 'related_standards' has been modified: Before: Gene Ontology Ontology for Biomedical Investigations Variation Ontology Ontology of Adverse Events Confidence Information Ontology After: Gene Ontology Ontology for Biomedical Investigations Variation Ontology Ontology of Adverse Events Confidence Information Ontology Disease Ontology Investigation Study Assay Tabular Neural ElectroMagnetic Ontologies Ontology of Microbial Phenotypes Added: Disease Ontology Investigation Study Assay Tabular Neural ElectroMagnetic Ontologies Ontology of Microbial Phenotypes Removed: 'dataProcesses' has been modified: Before: After: browse download submit new term releases Added: browse download submit new term releases Removed:
Edits to 'https://fairsharing.org/FAIRsharing.wvpgwn' by 'The FAIRsharing Team' at 17:01, 11 Jun 2019 (approved): 'related_standards' has been modified: Before: Gene Ontology Ontology for Biomedical Investigations Variation Ontology After: Gene Ontology Ontology for Biomedical Investigations Variation Ontology Ontology of Adverse Events Confidence Information Ontology Added: Ontology of Adverse Events Confidence Information Ontology Removed: 'onto_disciplines' has been modified: Before: Life Sciences After: Computational Biology Life Sciences Ontology and Terminology Added: Computational Biology Ontology and Terminology Removed: 'contactORCID' has been modified: Before: After: 0000-0001-9586-0780 'onto_domains' has been modified: Before: Evidence assay After: Evidence Experiment report Sample annotation Text mining assay literature curation study design Added: Experiment report Sample annotation Text mining literature curation study design Removed: 'publications' has been modified: Before: Standardized description of scientific evidence using the Evidence Ontology (ECO).|Chibucos MC,Mungall CJ,Balakrishnan R,Christie KR,Huntley RP,White O,Blake JA,Lewis SE,Giglio M|Database (Oxford)|2014 After: Standardized description of scientific evidence using the Evidence Ontology (ECO).|Chibucos MC,Mungall CJ,Balakrishnan R,Christie KR,Huntley RP,White O,Blake JA,Lewis SE,Giglio M|Database (Oxford)|2014 An evidence ontology for use in pathway/genome databases.|Karp PD,Paley S,Krieger CJ,Zhang P|Pac Symp Biocomput|2004 ECO, the Evidence & Conclusion Ontology: community standard for evidence information.|Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC|Nucleic Acids Res|2018 The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.|Chibucos MC,Siegele DA,Hu JC,Giglio M|Methods Mol Biol|2016 Added: An evidence ontology for use in pathway/genome databases.|Karp PD,Paley S,Krieger CJ,Zhang P|Pac Symp Biocomput|2004 ECO, the Evidence & Conclusion Ontology: community standard for evidence information.|Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC|Nucleic Acids Res|2018 The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.|Chibucos MC,Siegele DA,Hu JC,Giglio M|Methods Mol Biol|2016 Removed:
Edits to 'https://fairsharing.org/FAIRsharing.wvpgwn' by 'The FAIRsharing Team' at 14:17, 18 Jul 2018 (approved): 'homepage' has been modified: Before: http://www.evidenceontology.org/Welcome.html After: http://www.evidenceontology.org/
Edits to 'https://fairsharing.org/FAIRsharing.wvpgwn' by 'The FAIRsharing Team' at 20:00, 09 Sep 2016 (approved): 'homepage' has been modified: Before: http://purl.bioontology.org/ontology/ECO After: http://www.evidenceontology.org/Welcome.html
Edits to 'https://fairsharing.org/FAIRsharing.wvpgwn' by 'The FAIRsharing Team' at 21:23, 08 Sep 2016 (approved): 'description' has been modified: Before: "Evidence codes" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://purl.bioontology.org/ontology/ECO. This text was generated automatically. If you work on the project responsible for "Evidence codes" then please consider helping us by claiming this record and updating it appropriately. After: Evidence and Conclusions Ontology (ECO) provides the terminology for describing scientific evidence from a variety of biological research types including laboratory studies, literature data mining or computational analysis. ECO uses both 'evidence and assertion' methods in combination to support a research question and whether or not the hypothesis is computer-generated or a research personnel. Domain list has changed: Previous values: Assay|process|http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11025 Evidence information|property| Experiment|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2117 New values: Assay|process|http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#birnlex_11025 Evidence information|property| Experiment|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2117 Life Science|domain|
No XSD schemas defined
Conditions of UseApplies to: Data use
|submit new term||http://www.evidenceontology.org/submit_term_request/|
Standardized description of scientific evidence using the Evidence Ontology (ECO).
Chibucos MC,Mungall CJ,Balakrishnan R,Christie KR,Huntley RP,White O,Blake JA,Lewis SE,Giglio M
Database (Oxford) 2014
An evidence ontology for use in pathway/genome databases.
Karp PD,Paley S,Krieger CJ,Zhang P
Pac Symp Biocomput 2004
ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC
Nucleic Acids Res 2018
Models and Formats
No identifier schema standards defined
No metrics standards defined
Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.
Saccharomyces Genome Database
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
The Arabidopsis Information Resource
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways, and are curated from the primary scientific literature. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.
neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
Termini-Oriented Protein Function INferred Database
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites. Additionally, termini are annotated from user submitted lists of termini and inferred from user submitted lists of cleavage sites. As a protein-centric database, TopFIND presents a website for each protein isoform (organized around UniProt accession codes). These websites contain general protein information, such as organism, chromosome location, and proteins sequence. They then list position information such as specific termini evidences, known cleavage sites, sequence features and domains for each protein. In addition, TopFIND shows each protein in the context of the protease web, a network of proteases and their inhibitors, where a protease can cleave of other proteases and their inhibitors thus influencing their activity. All information in TopFIND can be filtered by a powerful filter engine that relies on rich annotation as to the origin of data in TopFIND. TopFIND can also be programmatically queried using the PSICQUIC or XML API. Recently, software tools were developed to enable quick access to TopFIND data for lists of termini obtained by, for example, proteomic termini screens (terminomics). TopFIND Explorer “TopFINDer” reports position specific protein information for protein termini, such as terminus evidences, prime and non-prime sequences, and protein domains affected by cleavage. TopFINDer further reports summary statistics for protein cleavage by known proteases. PathFINDer is a second tool that reports proteolytic paths from a query protease to identified protein substrates thus enabling the differentiation between direct and indirect protease substrates and yielding mechanistic insights into pathways based on existing information.
AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
Bgee DataBase for Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.
Gene Ontology Annotation Database
The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data.
Yeast Searching for Transcriptional Regulators and Consensus Tracking
YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.
Rat Genome Database
The Rat Genome Database is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. It provides easy access to corresponding human and mouse data for cross-species comparison and its comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.
Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
Pseudomonas Genome DB
The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
EcoCyc E. coli Database
EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc has been curated from 37,000 publications as of 2019. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").
The Zebrafish Information Network
The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.
Yeast Resource Center Public Data Repository
The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.
CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the community, the quality and detail of the stored data and the up-to-date nature of the stored information.
DisGeNET: a knowledge base for disease genomics
DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific literature, and covers the whole landscape of human diseases. The current version of DisGeNET (v7.0) contains 1,134,942 gene-disease associations (GDAs), between 21,671 genes and 30,170 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 369,554 variant-disease associations (VDAs), between 194,515 variants and 14,155 diseases, traits, and phenotypes. The data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, a REST API, and an R package.
SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.
Ascidian Network for In Situ Expression and Embryological Data
Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole embryo (anatomy, morphogenesis).
Immune Epitope Database
The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.
Open Targets is a data integration platform for access to and visualisation of potential drug targets associated with disease. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources.
A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
Bovine Genome Database
The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.
The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center for Bioinformatics (SfB) at the UiT The Arctic University of Norway. SfB is hosting the UiT node of ELIXIR Norway. The MarRef, MarDb, MarFun and MarCat contextual databases are built by compiling data from a number of public available sequence, taxonomy and literature databases in a semi-automatic fashion.
Heart Diseases related Noncoding RNA Database
The Heart Disease-related Non-coding RNAs Database (HDncRNA) provides information about common heart diseases and their related noncoding RNAs. The HDncRNA database contains manually annotated associations of ncRNAs with heart disease. Sources of data in this database are published articles, ncRNA databases and public RNA-seq datasets.
Drug Database for Inborn Errors of Metabolism
DDIEM - Drug Database for inborn errors of metabolism is a database on therapeutic strategies for inborn errors of metabolism. These strategies are classified by mechanism and outcome in DDIEM ontology. DDIEM uses this ontology to categorize the experimental treatments that have been proposed or applied. The database includes descriptions of the phenotypes addressed by the treatment and drugs participating in treatment and procedures.
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National Science Foundation (NSF), USA (Government body)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
U.S. Department of Energy (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
1458400 (National Science Foundation (NSF), USA)
DE-AC02-05CH11231 (U.S. Department of Energy)
R01 GM089636 (National Institutes of Health (NIH), Bethesda, MD, USA)
R01-HG02729- 01 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
U41-HG002223 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
U41HG008735 (National Institutes of Health (NIH), Bethesda, MD, USA)