Record updated: March 7, 2021, 8:42 p.m. by The FAIRsharing Team.

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 20:42, 07 Mar 2021 (approved):

	'supportLinks' has been modified:
		Before:
			TeSS training|https://tess.elixir-europe.org/materials/cath-gene3d
			email|Gene3D.Contact@gmail.com
			help|http://gene3d.biochem.ucl.ac.uk/examples
		After:
			TeSS training|https://tess.elixir-europe.org/materials/cath-gene3d
			email|Gene3D.Contact@gmail.com
			help|http://gene3d.biochem.ucl.ac.uk/examples
			online documentation|http://gene3d.biochem.ucl.ac.uk/about
		Added:
			online documentation|http://gene3d.biochem.ucl.ac.uk/about
		Removed:

	'standardsImplemented' has been modified:
		Before:
			Gene Ontology
			Molecular Interaction eXtensible Markup Language
			Distributed Sequence Annotation System
		After:
			Gene Ontology
			Molecular Interaction eXtensible Markup Language
			Distributed Sequence Annotation System
			Bioschemas
		Added:
			Bioschemas
		Removed:

	'tools' has been modified:
		Before:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
			MODELLER||https://salilab.org/modeller/
		After:
		Added:
		Removed:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
			MODELLER||https://salilab.org/modeller/

	'description' has been modified:
		Before: Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.
		After: Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are scanned against CATH HMMs to predict domain sequence boundaries and make homologous superfamily assignments. 

	'dataProcesses' has been modified:
		Before:
			Protein Search, data release, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=protein
			automated curation, data curation, 
			Family Search, data access, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=family
			download, data access, http://download.cathdb.info/gene3d/CURRENT_RELEASE/
			search, data access, 
			CATH Search Sequence scanning, data access, http://www.cathdb.info/search/by_sequence
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. , data versioning, 
		After:
			Protein Search, data access, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=protein
			Family Search, data access, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=family
			download, data release, ftp://orengoftp.biochem.ucl.ac.uk/gene3d/CURRENT_RELEASE/
			Genome Comparison, data access, http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. , data versioning, 
		Added:
			Protein Search, data access, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=protein
			download, data release, ftp://orengoftp.biochem.ucl.ac.uk/gene3d/CURRENT_RELEASE/
			Genome Comparison, data access, http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
		Removed:
			Protein Search, data release, http://gene3d.biochem.ucl.ac.uk/searchForm?mode=protein
			automated curation, data curation, 
			download, data access, http://download.cathdb.info/gene3d/CURRENT_RELEASE/
			search, data access, 
			CATH Search Sequence scanning, data access, http://www.cathdb.info/search/by_sequence

            

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 10:01, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Annotation
			Gene
			Genome
			Hidden Markov model (HMM)
			Life Science
			Protein interactions
			Protein structure
		After:
			Amino acid sequence
			Annotation
			Gene
			Genome
			Hidden Markov model (HMM)
			Life Science
			Protein domain
			Protein interactions
			Protein structure
		Added:
			Amino acid sequence
			Protein domain
		Removed:

            

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 17:25, 13 Aug 2018 (approved):

	'dataProcesses' has been modified:
		Before:
			Protein Search
			automated curation
			Family Search
			download
			search
			CATH Search Sequence scanning
		After:
			Protein Search
			automated curation
			Family Search
			download
			search
			CATH Search Sequence scanning
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. 
		Added:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. 
		Removed:

            

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 17:14, 13 Aug 2018 (approved):

	'description' has been modified:
		Before: Precalculated structural assignments for whole genomes.
		After: Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.

            

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 00:56, 02 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			University College London|http://www.ucl.ac.uk/smb|Maintains
			European Commission|http://ec.europa.eu/|Funds
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Institutes of Health|https://www.nih.gov|Funds
			Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London. WC1E 6BT, UK.|http://www.ucl.ac.uk/smb|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
		After:
			European Commission|http://ec.europa.eu/|Funds
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Institutes of Health|https://www.nih.gov|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			University College London|http://www.ucl.ac.uk/smb|Maintains
			Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London. WC1E 6BT, UK.|http://www.ucl.ac.uk/smb|Maintains
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
			National Institutes of Health|http://www.nih.gov|Funds
		Added:
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
			National Institutes of Health|http://www.nih.gov|Funds
		Removed:

	'related_databases' has been modified:
		Before:
			ProtoNet
			Statistical Torsional Angles Potentials of NMR Refinement Database
			Plant Transcription Factor Database
			CATH Protein Structure Classification
		After:
			IntAct molecular interaction database
			Pfam Protein Families
			ProtoNet
			Statistical Torsional Angles Potentials of NMR Refinement Database
			Plant Transcription Factor Database
			DrugBank
			Integrated resource of protein families, domains and functional sites
			Ensembl
			UniProt Knowledgebase
			CATH Protein Structure Classification
		Added:
			IntAct molecular interaction database
			Pfam Protein Families
			DrugBank
			Integrated resource of protein families, domains and functional sites
			Ensembl
			UniProt Knowledgebase
		Removed:

	'dataProcesses' has been modified:
		Before:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. We currently store only the current versions domain assignments.
			download
			three times a year releanse (dependent on the yearly releases of CATH)
			automated curation
			search
		After:
			Family Search
			download
			Protein Search
			automated curation
			search
			CATH Search Sequence scanning
		Added:
			Family Search
			Protein Search
			CATH Search Sequence scanning
		Removed:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. We currently store only the current versions domain assignments.
			three times a year releanse (dependent on the yearly releases of CATH)

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

	'publications' has been modified:
		Before:
			The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.|Yeats C., Lees J., Carter P., Sillitoe I., Orengo C., |Nucleic Acids Res.|2011
			Gene3D: merging structure and function for a Thousand genomes.|Lees J., Yeats C., Redfern O., Clegg A., Orengo C., |Nucleic Acids Res.|2010
		After:
			The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.|Yeats C., Lees J., Carter P., Sillitoe I., Orengo C., |Nucleic Acids Res.|2011
			Gene3D: merging structure and function for a Thousand genomes.|Lees J., Yeats C., Redfern O., Clegg A., Orengo C., |Nucleic Acids Res.|2010
			Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.|Das S,Lee D,Sillitoe I,Dawson NL,Lees JG,Orengo CA|Bioinformatics|2015
			Gene3D: Extensive prediction of globular domains in proteins.|Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J|Nucleic Acids Res|2017
		Added:
			Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.|Das S,Lee D,Sillitoe I,Dawson NL,Lees JG,Orengo CA|Bioinformatics|2015
			Gene3D: Extensive prediction of globular domains in proteins.|Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J|Nucleic Acids Res|2017
		Removed:

	'tools' has been modified:
		Before:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
		After:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
			MODELLER||https://salilab.org/modeller/
		Added:
			MODELLER||https://salilab.org/modeller/
		Removed:

            

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 15:09, 06 Sep 2016 (approved):

	'description' has been modified:
		Before: Precalculated structural assignments for whole genomes
		After: Precalculated structural assignments for whole genomes.