FAIR adoption, assessment and challenges at UniProt

García, Leyla; Bolleman, Jerven; Géhant, Sébastien; Redaschi, Nicole; Martin, Maria Jesus

doi:10.1038/s41597-019-0180-9

Cited by 13 publications

(9 citation statements)

References 6 publications

(5 reference statements)

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“…Important information of spike protein from published papers (Ahmed et al, 2020 ; Lan et al, 2020 ; Ou et al, 2020 ; Rabaan et al, 2020 ; Yan et al, 2020 ) and related databases such as UniProt (Garcia et al, 2019 ) and NCBI were extracted (Yang, 2020 ). Due to the effect of point mutations on the 3D structure, folding, and stability of a protein, it is expected that the immunogenicity of the spike could also be changed.…”

Section: Methodsmentioning

confidence: 99%

Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study

Gomari

Rostami

Omidi-Ardali

et al. 2021

Journal of Biomolecular Structure and Dynamics

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Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it.

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Section: Methodsmentioning

confidence: 99%

Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study

Gomari

Rostami

Omidi-Ardali

et al. 2021

Journal of Biomolecular Structure and Dynamics

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“…To further ensure our data is both human-readable and also computationally-tractable and continues to adhere to the FAIR principles ( 2 ), we are working to standardize the representation of all existing UniProt data on the functional impact of human variation. UniProtKB/Swiss-Prot has curated over 81 000 variants in 13,000 human protein sequence records from peer-reviewed literature, annotated with information on the functional impact and clinical significance, when known.…”

Section: Progress and New Developmentsmentioning

confidence: 99%

“…In recognition of the quality of our data, and the service we provide, UniProt was recognised as an ELIXIR Core Data Resource in 2017 ( 1 ) and received the CoreTrustSeal certification in 2020. The data resource fully supports the Findable, Accessible, Interoperable and Reusable (FAIR) data principles ( 2 ), for example by making data available in a number of community recognised formats, such as text, XML and RDF and via Application Programming Interfaces (API)s and File Transfer Protocol (FTP) downloads, providing stable and traceable identifiers for protein sequence and protein sequence features and by fully evidencing our data sources throughout. We have also reviewed and updated our data licencing policies.…”

Section: Introductionmentioning

confidence: 99%

UniProt: the universal protein knowledgebase in 2021

Bateman¹,

Martin²,

Orchard³

et al. 2020

Nucleic Acids Research

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5,314

3,195

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The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

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“…FAIR data from Uniprot [23] were combined with Ensembl FAIR data [24] in order to obtain the new datasets used in this study, which were uploaded and univocally identified on Zenodo, the open globally scoped repository (https://about.zenodo.org/principles/ (accessed on 16 February 2021)) under FAIR principle [22]. We described metadata identifying the digital object and the process used to integrate data.…”

Section: Discussionmentioning

confidence: 99%

Chromosome Walking: A Novel Approach to Analyse Amino Acid Content of Human Proteins Ordered by Gene Position

et al. 2021

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Notwithstanding the huge amount of detailed information available in protein databases, it is not possible to automatically download a list of proteins ordered by the position of their codifying gene. This order becomes crucial when analyzing common features of proteins produced by loci or other specific regions of human chromosomes. In this study, we developed a new procedure that interrogates two human databases (genomic and protein) and produces a novel dataset of ordered proteins following the mapping of the corresponding genes. We validated and implemented the procedure to create a user-friendly web application. This novel data mining was used to evaluate the distribution of critical amino acid content in proteins codified by a human chromosome. For this purpose, we designed a new methodological approach called chromosome walking, which scanned the whole chromosome and found the regions producing proteins enriched in a selected amino acid. As an example of biomedical application, we investigated the human chromosome 15, which contains the locus DYX1 linked to developmental dyslexia, and we found three additional putative gene clusters whose expression could be driven by the environmental availability of glutamate. The novel data mining procedure and analysis could be exploited in the study of several human pathologies.

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FAIR adoption, assessment and challenges at UniProt

Cited by 13 publications

References 6 publications

Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study

Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study

UniProt: the universal protein knowledgebase in 2021

Chromosome Walking: A Novel Approach to Analyse Amino Acid Content of Human Proteins Ordered by Gene Position

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