ZFIN

Publication

ZDB-PUB-120306-4

Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries

Authors:	UniProt-GOA
Journal:	Manually curated data 2011
Abstract:	Transitive assignment of GO terms based on the UniProtKB Subcellular Location vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to supply subcellular location information to UniProtKB entries in the SUBCELLULAR LOCATION lines. Terms from this vocabulary are applied automatically to UniProtKB/TrEMBL entries from the underlying nucleic acid databases and/or by the UniProt automatic annotation program. Further information on the UniProtKB automatic annotation program is available at http://www.uniprot.org/faq/45. When a UniProtKB Subcellular Location term describes a concept that is within the scope of the Gene Ontology, it is investigated to determine whether it is appropriate to map the term to an equivalent term in GO. The mapping between UniProtKB Subcellular Location terms and GO terms is carried out manually. Definitions and hierarchies of the terms in the two resources are compared and the mapping generated will reflect the most correct correspondence. The translation table between GO terms and UniProtKB Subcellular Location terms is maintained by the UniProt-GOA team and available at http://www.geneontology.org/external2go/spsl2go.

Matching Text:

Gene	...atf1
Related Gene Symbol	...atf1

Publication

ZDB-PUB-040217-1

ZGC Data Curation and Association in ZFIN by ZFIN Staff

Authors:	ZFIN Staff
Journal:	Semi-automated Curation 2004
Abstract:	The Zebrafish Gene Collection (http://zgc.nci.nih.gov/) contains full-length cDNA clones of expressed zebrafish genes. These cDNA sequences have been curated and associated with their encoding gene in ZFIN. In the case of genes novel to ZFIN, the associations were made after creating a new gene. Nomenclature for novel genes was assigned using the ZGC clone accession ID. This nomenclature will be revised as part of the ongoing curation process at ZFIN when additional information about these genes and their function becomes available. Nomenclature revisions also incorporate information from paralogous and orthologous sequences and through collaborative efforts with other databases. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-240305-9

Association of Ensembl transcripts with ZFIN genes

Authors:	ZFIN Staff
Journal:	Semi-automated Curation 2024
Abstract:	Transcripts that were annotated using Ensembl's automatic annotation pipeline and not previously identified in the manually curated Vega transcript set were associated with ZFIN genes to provide a comprehensive set of zebrafish transcripts from the GRCz11 assembly. Transcripts for Ensembl genes that have Ensembl Gene IDs unambiguously attributed with ZFIN genes are identified, have transcript records created and associated with genes in ZFIN. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-020724-1

Gene Ontology Annotation Through Association of InterPro Records with GO Terms

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2002
Abstract:	ZFIN's curation of data includes the assignment of Gene Ontology (GO) controlled vocabulary terms. Genes are annotated with terms from three ontologies (Molecular Function, Cellular Component, and Biological Process). These annotations have been assigned based on an automated association of InterPro records with GO terms using a translation table provided by GO. The same set of GO vocabulary terms are used by other species genomic databases (www.geneontology.org). This allows direct comparisons of genes among different species. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-030905-1

Curation of orthology data

Authors:	ZFIN Staff
Journal:	Manually curated data 2003
Abstract:	Orthology data citing this reference has been analyzed and annotated by a ZFIN scientific curator. Analyses include, but are not limited to, nucleotide and amino acid sequence comparison as well as conserved map location. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Matching Text:

Gene	...atf1
Related Gene Symbol	...atf1
Gene Full Name	...microcephalin 1......guanylate cyclase 1 soluble subunit beta 1

Publication

ZDB-PUB-020723-1

Gene Ontology Annotation Through Association of UniProt Keywords with GO Terms

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2002
Abstract:	ZFIN's curation of data includes the assignment of Gene Ontology (GO) controlled vocabulary terms. Genes are annotated with terms from three ontologies (Molecular Function, Cellular Component, and Biological Process). These annotations have been assigned based on an automated association of keywords from the UniProt database with GO terms using a translation table provided by GO. The same set of GO vocabulary terms are used by other species genomic databases (www.geneontology.org). This allows direct comparisons of genes among different species. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Matching Text:

Gene	...atf1
Related Gene Symbol	...atf1

Publication

ZDB-PUB-061101-1

Curation of Ensembl Database Links

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2006
Abstract:	Links to Ensembl gene records are established through automated data exchange between ZFIN and the Ensembl project. Ensembl gene identifiers are only included for ZFIN genes that are associated with a unique Ensembl gene record. Ensembl provides automated genome annotation and subsequent visualization of the genome. Details of this process are available here. Ensembl/Sanger associates these genes with cDNAs that match at least 90% of the identity of Ensembl gene. Association between the cDNAs and ZFIN genes are used to create links between Ensembl and ZFIN. To obtain more detailed information about this process or to send comments, please contact ZFIN zfinadmn@zfin.org.

Publication

ZDB-PUB-020723-3

Curation of NCBI Gene Data Via Shared RNA Sequence IDs

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2002
Abstract:	Links to NCBI data are established through a collaboration between ZFIN and NCBI staff. ZFIN gene records are matched with NCBI Gene records based on shared RNA sequence accession numbers. Where there are no conflicts, links to the NCBI Gene record are created in ZFIN. RefSeqs, RefPepts, GenPepts, UniGene and sequence accession numbers in the NCBI Gene record that are not found in ZFIN are also added. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-020723-5

Scientific Curation

Authors:	ZFIN Staff
Journal:	Manually curated data 2002
Abstract:	Data citing this reference have been reviewed and annotated by a ZFIN scientific curator. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-110330-1

Annotation inferences using phylogenetic trees

Authors:	Gaudet, P., Livstone, M., Thomas, P., The Reference Genome Project
Journal:	Automated Data Submission 2010
Abstract:	The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes.To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool). url: http://gocwiki.geneontology.org/index.php/PAINT

Publication

ZDB-PUB-030703-1

Curation of VEGA Database Links

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2003
Abstract:	Links to VEGA records are established through a collaboration between ZFIN and Sanger Institute staff. VEGA identifiers for genes are added to ZFIN records automatically via established ZFIN/Sanger relationships. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-130213-1

Semi-automated association of ENSDARG identifiers with ZFIN genes for the ZMP project

Authors:	ZFIN Staff
Journal:	Semi-automated Curation 2013
Abstract:	In order to load the Zebrafish Mutation Project (ZMP) mutants into ZFIN, ENSDARG identifiers were associated with ZFIN genes semi-automatically, based on a collaboration between Sanger staff and ZFIN. To obtain more detailed information about this process or send comments, please contact ZFIN.

Publication

ZDB-PUB-170810-14

Curation of PANTHER Gene IDs

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2017
Abstract:	Links to PANTHER records are established through a collaboration between ZFIN and PANTHER staff. PANTHER accession numbers are added to ZFIN records electronically via associations established by PANTHER. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Publication

ZDB-PUB-230615-71

Automated Curation of UniProt Database Links

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2023
Abstract:	A data exchange between ZFIN and UniProt matches nucleotide sequences with their protein products. This effort results in the automated addition of UniProt IDs and related data content to ZFIN gene records. To obtain more detailed information about this process or to send comments, please contact ZFIN.

Matching Text:

Gene Full Name

...ALG2 alpha-1,3/1,6-mannosyltransferase......transglutaminase 1 like 1

Publication

ZDB-PUB-200103-6

Addition of links from ZFIN to Expression Atlas

Authors:	ZFIN Staff
Journal:	Semi-automated Curation 2020
Abstract:	The EBI Expression Atlas provides access to and visualization of high throughput data sets. Links from ZFIN gene pages to the Expression Atlas have been added by incorporation of the same link set identified at the Alliance of Genome Resources. The links in ZFIN are updated monthly to synchronize with the same set of links at the Alliance. If you would like more information about this process, please contact us at zfinadmn@zfin.org.

Publication

ZDB-PUB-171009-1

Curation of Alliance of Genome Resources Database Links

Authors:	ZFIN Staff
Journal:	Automated Data Submission 2017
Abstract:	Links to the Alliance of Genome Resources gene and disease data pages are established through an automated data exchange. The Alliance of Genome Resources links are added automatically to ZFIN gene and disease data pages via established ZFIN/Alliance of Genome Resources relationships. To obtain more detailed information about this process or to send comments, please contact ZFIN.