Evidence map›Paper›PMID 32034905›Full record

ArticleGigaScience2020

HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes.

Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea H Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi and 4 more

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Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Jerven BollemanSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Edouard de CastroSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Delphine BaratinSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Sebastien GehantSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Beatrice A CucheSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Andrea H AuchinclossSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Elisabeth CoudertSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Chantal HuloSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Patrick MassonSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Ivo PedruzziSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Catherine RivoireSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Ioannis XenariosSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Nicole RedaschiSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
Alan BridgeSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

Funding

UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's DiseaseU24HG007822 · NHGRI · GEORGETOWN UNIVERSITY · PI Alex Bateman, Alan James Bridge · 2018 to 2026
$53.0M
NHGRI NIH HHS U24 HG007822
6 · The paper itself

Abstract

backgroundGenome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.

resultsHere we demonstrate one approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline.

conclusionsHAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.

Indexed as

AnimalsGenomicsHumansMolecular Sequence AnnotationSequence Analysis, DNASequence Analysis, ProteinSoftwarefunctionpredictionproteinSPARQL

Identifiers

PMID32034905
PMCPMC7007698

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.