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Curation and ISA representation of a SARS-Cov2/Covid-19 Proteomics Dataset - PXD107710 - ISA representation

Curation and ISA representation of a SARS-Cov2/Covid-19 Proteomics Dataset deposited in PRIDE database with accession number: PXD107710 ISA-Tab annotation for the  "SARS-CoV-2 infected host cell proteomics reveal potential therapy targets" publication.  Github repository: <a href="https://github.com/ISA-tools/PXD017710">https://github.com/ISA-tools/PXD017710</a> This is part of an effort to (re-)annotate: <a href="https://dx.doi.org/10.21203/rs.3.rs-17218/v1">https://dx.doi.org/10.21203/rs.3.rs-17218/v1</a> Additional work done as part of: <ol> <li> <a href="https://github.com/virtual-biohackathons/covid-19-bh20">https://github.com/virtual-biohackathons/covid-19-bh20</a></li> <li> <a href="https://github.com/virtual-biohackathons/covid-19-bh20/wiki/FairData">https://github.com/virtual-biohackathons/covid-19-bh20/wiki/FairData</a></li> </ol> Proteomics data Available from PRIDE at <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD017710]">https://www.ebi.ac.uk/pride/archive/projects/PXD017710</a> and [<a href="https://massive.ucsd.edu/ProteoSAFe/result.jsp?task=334df9b4f1af4501bca0a2aa63278a7d&view=display_metadata_results&file=f.RMSV000000308%2F2020-03-22_nuno_334df9b4%2Fmetadata%2FMSV000085096_SARS-CoV-2_proteome_translatome.csv#%7B%22table_sort_history%22%3A%22_dyn_%23Condition_asc%22%7D">MassIVE/CCMS Maestro+MSstats reanalysis of MSV000085096 / PXD017710</a>] ISA-Tab representation: Rationale: Demonstrate suitability of the ISA format for representing MS based protein profiling experiment with more granularity and details, thus providing a better representation of the experiment design. The formatting and re-annotation are based on information extracted from: - the original publication - the supplementary tables available from the publishers site - the 'filtered-results.csv' helper file as supplied to @sneumann during the <a href="http://www.psidev.info/hupo-psi-meeting-2020">HUPO-PSI meeting March 2020</a> Viewing the ISA-tab formatted and re-annotated PXD017710 with I<a href="https://isa-tools.org/PXD017710/isaviewer-demo.html)">SATab-Viewer</a> Viewing the ISA-tab formatted and re-annotated PXD017710 locally, do the following: ```bash python -m http.server 8000 ``` Then point your browser to `http://0.0.0.0:8000/isaviewer-demo.html` Curation tasks performed: * initial structure of the study design in ISA format: * linkage of Proteome and Translatome data (supplementary material) to ISA assay tables (via Derived Data File) * processing the Proteome and Translatome data (supplementary material) with python pandas library to generate the following csv files:     - proteome_intensities_long_table_ggplot2.txt     - proteome_diffanal_ratio_pvalue_long_table_ggplot2.txt     - translatome_intensities_long_table_ggplot2.txt         - translatome_diffanal_ratio_pvalue_long_table_ggplot2          The files are `long table` corresponding to a `melt` on the Excel file originally generated by the users and can be readily loaded in R ggplot2 library for graphical representation.     The statistical relevant elements have been annotated with the <a href="http://stato-ontology.org/">STATO ontology</a> and the tables comply with a Frictionless.io Data Package.     The jupyter notebook for the transformation is available. * conversion of raw data to mzML format: detailed in <a href="https://github.com/ISA-tools/PXD017710">https://github.com/ISA-tools/PXD017710</a> install docker:  ```bash         >brew update         >brew install docker ``` sign in to docker ```bash         >docker start         >docker login ``` pull docker container for ProteoWizard: ```bash >docker pull chambm/pwiz-i-agree-to-the-vendor-licenses ``` :warning: be sure to sign-up and login to https://hub.docker.com/ in order to be able to reach https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses run the pwiz tool from the container over the raw data: ```bash  docker run -it --rm -e WINEDEBUG=-all -v /Users/Downloads/PXD017710/raw/:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/*.raw --mzML ``` * ontology markup for:     * declaration of independent variables as ISA Study Factors:{biological agent, dose, time point, replicate} ->OBI     * Taxonomic information (host cells and virus) -> NCBITaxonomy     * Cell line: CaCo-2 cells -> Cell Line Ontology     * Disease: Colon Cancer -> Human Phenotype Ontology     * MS specific aspect (TMT reagent, instrument ... ) -> PSI-MS     * Statistical Tests -> STATO Unresolved curatorial issues:  1. ambiguities related to Tandem Mass Tag labelling protocol     - the publication mentions TMT11 (see Figure 2 in https://www.researchsquare.com/article/rs-17218/v1)     - the information available from PRIDE mentions TMT6 (https://www.ebi.ac.uk/pride/archive/projects/PXD017710)     This may require another round of annotation on the TMT agents and fractions in the ISA a_assay representation  2. SARS-Cov2 isolate: no clear NCBI Taxonomic anchoring and unclear origin: -> the markup is made to the parent class (as of 06.04.2020) Release and packaging as a BDBAG: The tgz file associated with this upload has been producing using <a href="https://github.com/fair-research/bdbag">https://github.com/fair-research/bdbag</a>. It contains several manifest files detailing metadata and data files, providing md5 and sha256 checksums. Github repository: <a href="https://github.com/ISA-tools/PXD017710">https://github.com/ISA-tools/PXD017710</a>

ShareScore

36/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 16
Reuse readiness: 0
Engagement: 8

Topics

FAIR data Proteomics mass spectrometry SARS-Cov2 Covid-19 Caco2 cell line treated versus control intervention design ISA format STATO ontology bdbag FAIRsharing

Curation and ISA representation of a SARS-Cov2/Covid-19 Proteomics Dataset - PXD107710 - ISA representation

Score breakdown

Topics

Your academic CV and NIH biosketch