Evidence map›Paper›PMID 32716361›Full record

ArticleJournal of Alzheimer's disease : JAD2020

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.

Lionel Breuza, Cecilia N Arighi, Ghislaine Argoud-Puy, Cristina Casals-Casas, Anne Estreicher, Maria Livia Famiglietti, George Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of Alzheimer's disease : JAD, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
  2. NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024
    Article
  3. ACS chemical biology · 2022
    Article
  4. Article
  5. Article
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

25 authors.

Lionel BreuzaSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Cecilia N ArighiProtein Information Resource, Georgetown University Medical Center, Washington, DC, USA.
Ghislaine Argoud-PuySwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Cristina Casals-CasasSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Anne EstreicherSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Maria Livia FamigliettiSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
George GeorghiouEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
Arnaud GosSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Nadine Gruaz-GumowskiSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Ursula HinzSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Nevila Hyka-NouspikelSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Barbara KramarzFunctional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), London, UK.
Ruth C LoveringFunctional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), London, UK.
Yvonne LussiEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
Michele MagraneEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
Patrick MassonSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Livia PerfettoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
Sylvain PouxSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Milagros Rodriguez-LopezEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
Christian StoeckertPerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Shyamala SundaramSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.
Li-San WangPerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Elizabeth WuAlzforum, Cambridge, MA, USA.
Sandra OrchardEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, UK.
IMEx Consortium, UniProt Consortium

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
Department of HealthNHGRI NIH HHS U24 HG007822Wellcome TrustWellcome Trust 212925/Z/18/Z
6 · The paper itself

Abstract

backgroundThe analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured biological data described in free-text journal articles and converting this into more structured, computationally-accessible forms. This enables analyses such as functional enrichment of sets of genes/proteins using the Gene Ontology, and makes the searching of data more productive by managing issues such as gene/protein name synonyms, identifier mapping, and data quality.

objectiveTo undertake a coordinated annotation update of key public-domain resources to better support Alzheimer's disease research.

methodsWe have systematically identified target proteins critical to disease process, in part by accessing informed input from the clinical research community.

resultsData from 954 papers have been added to the UniProtKB, Gene Ontology, and the International Molecular Exchange Consortium (IMEx) databases, with 299 human proteins and 279 orthologs updated in UniProtKB. 745 binary interactions were added to the IMEx human molecular interaction dataset.

conclusionThis represents a significant enhancement in the expert curated data pertinent to Alzheimer's disease available in a number of biomedical databases. Relevant protein entries have been updated in UniProtKB and concomitantly in the Gene Ontology. Molecular interaction networks have been significantly extended in the IMEx Consortium dataset and a set of reference protein complexes created. All the resources described are open-source and freely available to the research community and we provide examples of how these data could be exploited by researchers.

Indexed as

Databases, ProteinExpert SystemsPublic SectorAlzheimer DiseaseComputational BiologyHumansProtein Interaction MapsAlzheimer’s diseaseCytoscape network analysisdatabasedata curationneurobiologyprotein

Identifiers

PMID32716361
PMCPMC7592670

What OpenQuestion holds

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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.