This is GlycoQL

  1. Catherine Hayes
  2. Vincenzo Daponte
  3. Julien Mariethoz
  4. Frederique Lisacek

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Abstract

Motivation

We have previously designed and implemented a tree-based ontology to represent glycan structures with the aim of searching these structures with a glyco-driven syntax. This resulted in creating the GlySTreeM knowledge-base as a linchpin of the structural matching procedure and we now introduce a query language, called GlycoQL, for the actual implementation of a glycan structure search.

Results

The methodology is described and illustrated with a use-case focused on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike protein glycosylation. We show how to enhance site annotation with federated queries involving UniProt and GlyConnect, our glycoprotein database.

Availability and implementation

https://glyconnect.expasy.org/glycoql/.

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  1. Version published to 10.1093/bioinformatics/btac500
  2. ScreenIT

    SciScore for 10.1101/2022.04.14.488348: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    These structures are reported for a number of glycosylation sites across experimentally different recombinant versions of the protein, using three expression systems, namely, HEK293 (human embryonic kidney), BTI-Tn-5B1-4 (insect cell) and CHO (Chinese Hamster Ovary).
    HEK293
    suggested: None
    Software and Algorithms
    SentencesResources
    The parsing algorithm incorporating the semantic choices proper to GlycoQL is implemented as a Python module based on RdfLib (Krech (2006)).
    Python
    suggested: (IPython, RRID:SCR_001658)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.04.14.488348v1 on bioRxiv