ArticleGenome research2004
The otter annotation system.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed.
- Apollo 3: Multi-Species Genome Curation.bioRxiv : the preprint server for biology · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.Nature methods · 2024Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.bioRxiv : the preprint server for biology · 2023Article
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.BMC genomics · 2020Article
- Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci.Immunogenetics · 2018Article
- The pig X and Y Chromosomes: structure, sequence, and evolution.Genome research · 2016Article
- Current transcriptomics in pig immunity research.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Review
- Comprehensive comparative homeobox gene annotation in human and mouse.Database : the journal of biological databases and curation · 2015Article
- Structural and functional annotation of the porcine immunome.BMC genomics · 2013Article
- ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.BioMed research international · 2013Article
- Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence.BMC genomics · 2012Article
- The GENCODE pseudogene resource.Genome biology · 2012Article
- GENCODE: the reference human genome annotation for The ENCODE Project.Genome research · 2012Article
- The importance of identifying alternative splicing in vertebrate genome annotation.Database : the journal of biological databases and curation · 2012Article
- Article
- Community gene annotation in practice.Database : the journal of biological databases and curation · 2012Article
- Pseudogene: lessons from PCR bias, identification and resurrection.Molecular biology reports · 2011Article
- Dalliance: interactive genome viewing on the web.Bioinformatics (Oxford, England) · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly even more important, is the requirement to curate and improve this annotation in the light of future data. For this to be possible, there is a need for tools to access and manage the annotation. Ensembl provides an excellent means for storing gene structures, genome features, and sequence, but it does not support the extra textual data necessary for manual annotation. We have extended Ensembl to create the Otter manual annotation system. This comprises a relational database schema for storing the manual annotation data, an application-programming interface (API) to access it, an extensible markup language (XML) format to allow transfer of the data, and a server to allow multiuser/multimachine access to the data. We have also written a data-adaptor plugin for the Apollo Browser/Editor to enable it to utilize an Otter server. The otter database is currently used by the Vertebrate Genome Annotation (VEGA) site (http://vega.sanger.ac.uk), which provides access to manually curated human chromosomes. Support is also being developed for using the AceDB annotation editor, FMap, via a perl wrapper called Lace. The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.