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CHEMical INFormation Ontology

Abbreviation: CHEMINF

General Information

The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed.

Homepage https://github.com/semanticchemistry/semanticchemistry

Countries that developed this resource Netherlands

Created in 2010

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: CHEMINF; CHEMical INFormation Ontology; DOI: https://doi.org/10.25504/FAIRsharing.sjhvyy; Last edited: July 9, 2019, 10:24 a.m.; Last accessed: Oct 24 2021 10:39 a.m.

Publication for citation The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. Hastings J,Chepelev L,Willighagen E,Adams N,Steinbeck C,Dumontier M; PLoS One ; 2011; 10.1371/journal.pone.0025513;

Record updated: July 8, 2019, 3:23 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.sjhvyy' by 'The FAIRsharing Team' at 15:23, 08 Jul 2019 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Chemical Information Ontology (CHEMINF) Administrators|https://github.com/semanticchemistry/semanticchemistry|Maintains
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
			Uppsala University, Sweden|http://www.uu.se|Maintains,Funds
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Uppsala University, Sweden|http://www.uu.se|Funds
			Chemical Information Ontology (CHEMINF) Administrators|https://github.com/semanticchemistry/semanticchemistry|Maintains
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
		Added:
			Uppsala University, Sweden|http://www.uu.se|Funds
		Removed:
			Uppsala University, Sweden|http://www.uu.se|Maintains,Funds

	'onto_disciplines' has been modified:
		Before:
			Biochemistry
			Chemistry
			Life Sciences
		After:
			Biochemistry
			Chemistry
			Life Sciences
			Ontology and Terminology
		Added:
			Ontology and Terminology
		Removed:

	'contactORCID' has been modified:
		Before: 
		After: 0000-0001-7542-0286

Edits to 'https://fairsharing.org/FAIRsharing.sjhvyy' by 'The FAIRsharing Team' at 13:16, 14 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Chemical Information Ontology (CHEMINF) Administrators|http://code.google.com/p/semanticchemistry/|Maintains
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
			Uppsala University, Sweden|http://www.uu.se|Maintains
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Chemical Information Ontology (CHEMINF) Administrators|http://code.google.com/p/semanticchemistry/|Maintains
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
			Uppsala University, Sweden|http://www.uu.se|Maintains,Funds
		Added:
			Uppsala University, Sweden|http://www.uu.se|Maintains,Funds
		Removed:
			Uppsala University, Sweden|http://www.uu.se|Maintains

	'supportLinks' has been modified:
		Before:
			online documentation|https://github.com/egonw/semanticchemistry
		After:
			forum|https://github.com/semanticchemistry/semanticchemistry/issues
		Added:
			forum|https://github.com/semanticchemistry/semanticchemistry/issues
		Removed:
			online documentation|https://github.com/egonw/semanticchemistry

	'description' has been modified:
		Before:   The Chemical Information Ontology (CHEMINF), is a formal ontology pertaining to chemical information entities that is being developed collaboratively within the context of the OBO Foundry.  The ontology  is implemented with the Web Ontology Language (OWL2). ChEMINF includes; chemical graphs, chemical descriptors, as well as algorithms and chemical data representation formalisms and formats.
		After: The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed.

	'licences' has been modified:
		Before:
			Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0)|https://creativecommons.org/licenses/by-sa/3.0/|Data
		After:
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
		Added:
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
		Removed:
			Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0)|https://creativecommons.org/licenses/by-sa/3.0/|Data

	'yearOfCreation' has been modified:
		Before: None
		After: 2010

	'miriam_id' has been modified:
		Before: None
		After: 

	'homepage' has been modified:
		Before: http://purl.bioontology.org/ontology/CHEMINF
		After: https://github.com/semanticchemistry/semanticchemistry

Edits to 'https://fairsharing.org/FAIRsharing.sjhvyy' by 'The FAIRsharing Team' at 11:15, 31 Aug 2016 (approved):

	'description' has been modified:
		Before: "CHEMical INFormation Ontology" 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/CHEMINF. This text was generated automatically. If you work on the project responsible for "CHEMical INFormation Ontology" then please consider helping us  by claiming this record  and updating it appropriately.
		After:   The Chemical Information Ontology (CHEMINF), is a formal ontology pertaining to chemical information entities that is being developed collaboratively within the context of the OBO Foundry.  The ontology  is implemented with the Web Ontology Language (OWL2). ChEMINF includes; chemical graphs, chemical descriptors, as well as algorithms and chemical data representation formalisms and formats. Domain list has changed:  Previous values: Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Chemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100618 Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Chemical.owl#CHEBI_24431 New values:  Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Chemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100618 Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Chemical.owl#CHEBI_24431 Life Science|domain| Organisations have changed:  Previous values: CHEMINF administrators New values:  CHEMINF administrators National Centre for Biomedical Ontology Biotechnology and Biological Sciences Research Council|UK Uppsala University|Sweden Grants have changed:  Previous values: New values:  BB/G022747/1 KoF 07

In Collections

Chemistry

ISO/CD 20691 Collection - DRAFT

Support

General

forum

GitHub Issue Tracker

Additional Information

Contact

Egon Willighagen ORCID

External Links

Bioportal	http://bioportal.bioontology.org/ontologies/CHEMINF
OBO	http://obofoundry.org/ontology/cheminf.html

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Publications

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Hastings J,Chepelev L,Willighagen E,Adams N,Steinbeck C,Dumontier M
PLoS One 2011

View Paper (PubMed) View Publication

CHEMINF Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (4)

ChEMBL
ChEMBL is an open, manually-curated, large-scale bioactivity database containing information from medicinal chemistry literature. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

PubChem
PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.

OBO Foundry
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.

DNA Modification Database
DNAmod is an open-source database (https://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. The database annotates the chemical properties and structures of all curated modified DNA bases, and a much larger list of candidate chemical entities. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Uppsala University, Sweden (University)

Maintains

Chemical Information Ontology (CHEMINF) Administrators (Consortium) Lead
National Center for Biomedical Ontology (NCBO), Stanford, CA, USA (Research institute)

Grant Number(s)

BB/G022747/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
KoF 07 (Uppsala University, Sweden)

CHEMical INFormation Ontology

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