BCO creation for 2.5

[kmartinez834]

BCO ID	Dataset Name	Creator Name	Notes
GLY_000965	chicken_proteoform_glycosylation_sites_uniprotkb.csv	Urnisha
GLY_000966	chicken_protein_ncbi_linkouts.csv	Urnisha
GLY_000967	chicken_protein_genelocus.csv	Urnisha
GLY_000993	chicken_protein_info_uniprotkb.csv	Urnisha
GLY_000994	chicken_protein_genenames_uniprotkb.csv	Urnisha
GLY_000995	chicken_protein_function_refseq.csv	Urnisha
GLY_000989	chicken_protein_citations_uniprotkb.csv	Kate
GLY_000990	chicken_protein_altnames.csv	Kate
GLY_001019	human_proteoform_citations_glycosylation_sites_embl.csv	Karina
GLY_000996	chicken_protein_xref_oglcnac_atlas.csv	Urnisha
GLY_000991	chicken_protein_xref_rhea.csv	Kate
GLY_001024	chicken_protein_glycohydrolase.csv	Jingyue
GLY_000979	chicken_proteoform_glycosylation_sites_literature.csv	Jingyue
GLY_000997	chicken_protein_info_refseq.csv	Urnisha
GLY_001021	mouse_proteoform_citations_glycosylation_sites_embl.csv	Karina
GLY_000998	chicken_protein_masterlist.csv	Urnisha
GLY_000960	human_proteoform_glycosylation_sites_diabetes_glycomic.csv	Karina
GLY_000980	chicken_proteoform_glycosylation_sites_glyconnect.csv	Jingyue
GLY_000982	chicken_proteoform_citations_phosphorylation_sites_uniprotkb.csv	Jingyue
GLY_000992	chicken_protein_xref_brenda.csv	Kate
GLY_001001	chicken_protein_xref_bgee.csv	Kate
GLY_000889	mouse_proteoform_glycosylation_sites_embl.csv	Karina
GLY_001002	chicken_protein_proteinnames_refseq.csv	Kate
GLY_000983	chicken_protein_xref_refseq.csv	Jingyue
GLY_000984	chicken_protein_transcriptlocus.csv	Jingyue
GLY_000985	chicken_protein_xref_kegg.csv	Jingyue
GLY_000986	chicken_protein_go_annotation.csv	Jingyue
GLY_001003	chicken_proteoform_citations_glycation_sites_uniprotkb.csv	Kate
GLY_001027	human_proteoform_citations_glycosylation_sites_pdc_ccrc.csv	Karina
GLY_000987	chicken_protein_participants_reactome.csv	Jingyue
GLY_001008	chicken_protein_submittednames.csv	Jingyue
GLY_001009	chicken_proteoform_glycosylation_sites_pdb.csv	Jingyue
GLY_001006	chicken_protein_xref_intact.csv	Kate
GLY_001012	chicken_protein_xref_cdd.csv	Jingyue	I didn't find the template on data.glygen.org
GLY_001010	chicken_protein_citations_refseq.csv	Jingyue
GLY_001013	chicken_protein_recnames.csv	Jingyue
GLY_001015	chicken_proteoform_citations_glycosylation_sites_uniprotkb.csv	Jingyue
GLY_001022	chicken_protein_reactions_reactome.csv	Jingyue
GLY_001020	chicken_protein_xref_geneid.csv	Jingyue
GLY_001023	chicken_proteoform_phosphorylation_sites_uniprotkb.csv	Jingyue
GLY_000888	human_proteoform_glycosylation_sites_embl.csv	Karina
GLY_001025	chicken_protein_reactions_rhea.csv	Jingyue
GLY_000961	human_proteoform_glycosylation_sites_pdc_ccrc.csv	Karina
GLY_000978	chicken_protein_xref_orthodb.csv	Luke
GLY_000977	chicken_protein_pro_annotation.csv	Luke
chicken_protein_signalp_peptidesequences.fasta	Not required. part of chicken_protein_signalp_annotation.csv
GLY_000976	chicken_proteoform_glycosylation_sites_literature_mining.csv	Luke
GLY_001007	chicken_protein_site_annotation_uniprotkb.csv	Kate
GLY_000975	chicken_protein_binary_interactions.csv	Luke
GLY_000974	chicken_protein_xref_pro.csv	Luke
GLY_000973	chicken_protein_xref_glyconnect.csv	Luke
GLY_000972	chicken_protein_glycosylation_motifs.csv	Luke
GLY_000971	chicken_protein_canonicalsequences.fasta	Luke
GLY_001016	human_proteoform_citations_glycosylation_sites_diabetes_glycomic.csv	Karina
chicken_protein_signalp_fullsequences.fasta	not required. Part of chicken_protein_signalp_annotation.csv
GLY_000970	chicken_protein_xref_oma.csv	Luke
chicken_protein_signalp_cleavedsequences.fasta	Not required. Part of chicken_protein_signalp_annotation.csv
GLY_000969	chicken_protein_xref_panther.csv	Luke
GLY_001011	chicken_proteoform_citations_glycosylation_sites_oglcnac_mcw.csv	Kate
GLY_000968	chicken_protein_pathways_reactome.csv	Luke
GLY_001014	chicken_protein_signalp_annotation.csv	Kate
GLY_001026	chicken_proteoform_citations_phosphorylation_sites_iptmnet.csv	kate
GLY_001028	chicken_protein_citations_reactome.csv	Cyrus
GLY_001029	chicken_protein_enzyme_annotation_uniprotkb.csv	Cyrus
GLY_001030	chicken_protein_ptm_annotation_uniprotkb.csv	Cyrus
GLY_001031	chicken_protein_xref_pfam.csv	Cyrus
GLY_001032	chicken_proteoform_citations_glycosylation_sites_oglcnac_atlas.csv	Cyrus
GLY_001033	chicken_proteoform_phosphorylation_sites_iptmnet.csv	Cyrus
GLY_001034	chicken_protein_ntdata.nt	Cyrus
GLY_001035	chicken_protein_function_uniprotkb.csv	Cyrus
GLY_001036	chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv	Cyrus
GLY_001018	chicken_protein_genenames_refseq.csv	Kate
GLY_001037	chicken_protein_xref_uniprotkb.csv	Cyrus
GLY_001038	chicken_protein_participants_rhea.csv	Cyrus
GLY_001039	chicken_protein_sequenceinfo.csv	Cyrus
GLY_000999	chicken_protein_glycosyltransferase.csv	Urnisha
GLY_001000	chicken_protein_xref_pdb.csv	Urnisha
GLY_001004	chicken_protein_xref_interpro.csv	Urnisha
GLY_001005	chicken_protein_allsequences.fasta	Urnisha
GLY_001040	chicken_protein_xref_cazy.csv	Cyrus
GLY_001041	chicken_protein_xref_reactome.csv	Cyrus
GLY_001042	chicken_protein_xref_chembl.csv	Cyrus
GLY_001045	human_proteoform_ml_ready_diabetes_glycomic.csv	Karina
GLY_001046	human_proteoform_ml_ready_pdc_ccrc.csv	Karina
GLY_001044	yeast_protein_pathways_reactome.csv	Karina
GLY_001043	yeast_protein_xref_reactome.csv	Karina
GLY_001047	rat_protein_matrixdb.csv	Karina
GLY_001048	rat_protein_citations_matrixdb.csv	Karina

[kmartinez834]

Please claim a chunk of these BCOs to create by end of next week (5/17)

[katewarner]

Perhaps it would be good to add another column to the table, where we can add our names to the BCOs were working on?

[kmartinez834]

@katewarner you can use the "Creator name" column for those you'll work on, thanks!

[katewarner]

@kmartinez834 Sorry, I could only see the first two columns in the ticket - I'm an idiot :-D

[jeet-vora]

Please claim atleast 12 BCOs by Monday 05/13 or they will be automatically assigned to you.

[JingyueWu]

@jeet-vora I accidentally created Chicken Glycosylation Sites (GlyConnect) BCO twice, can you please delete https://biocomputeobject.org/GLY_000981/DRAFT?

[jeet-vora]

@JingyueWu I do not have permission to delete it. @tiwa1154 has done it.

[kmartinez834]

Make sure BCOs are in line with #1091

[kmartinez834]

@JingyueWu @CyrusAY can you take a look at your BCOs below? The following are resulting in errors:

$ python3 /software/glygen/check-bco2filename-mapping.py | grep ERROR
NO-BCO,chicken_protein_glycohydrolase.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_literature.csv,ERROR,in_fs
NO-BCO,chicken_protein_submittednames.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_pdb.csv,ERROR,in_fs
NO-BCO,chicken_protein_xref_cdd.csv,ERROR,in_fs
NO-BCO,chicken_protein_citations_refseq.csv,ERROR,in_fs
NO-BCO,chicken_protein_recnames.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_citations_glycosylation_sites_uniprotkb.csv,ERROR,in_fs
NO-BCO,chicken_protein_reactions_reactome.csv,ERROR,in_fs
NO-BCO,chicken_protein_xref_geneid.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_phosphorylation_sites_uniprotkb.csv,ERROR,in_fs
NO-BCO,chicken_protein_reactions_rhea.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_citations_glycosylation_sites_oglcnac_atlas.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv,ERROR,in_fs

[kmartinez834]

@rykahsay we need to fix a few BCOS (above), and I'm adding more details to my ML ready BCOs - do you mind waiting til EOB Monday to to create the BCO objects?

[CyrusAY]

Last two of the BCO that showed error were mine.

Fixed chicken_proteoform_citations_glycosylation_sites_oglcnac_atlas.csv

Updating the IO domain of chicken_proteoform_glycosylation_sites_literature_mining_manually_verified.csv (GLY_001036). Which of the following datasets should I include as the input?

Update: fixed

[kmartinez834]

@CyrusAY you can actually leave the input domain blank (or as-is). Robel will override it programmatically. Can you verify that the output domain is correct? Looks like it's currently human instead of chicken

[CyrusAY]

GLY_000979 | chicken_proteoform_glycosylation_sites_literature.csv should not be included in the chicken dataset. It is based off literatures specific to human only.

Usability domain reads:

The dataset provides information on N-glycosylation sites on Chicken proteins. The data has been processed from the supplementary material from 2 publications (1. "Deeb, S. J., Cox, J., Schmidt-Supprian, M., & Mann, M. (2013). N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes. Molecular & Cellular Proteomics, 13(1), 240-251. doi:10.1074/mcp.m113.033977" 2. "Boersema, P. J., Geiger, T., Winiewski, J. R., & Mann, M. (2012). Quantification of the N-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Chicken Blood Samples. Molecular & Cellular Proteomics, 12(1), 158-171. doi:10.1074/mcp.m112.023614"). The listed proteins (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000001).

Both literatures (the keyword 'human' is automatically changed to 'chicken' in the latter) were focusing on cancer patients.

On data.glygen.org there is another sarscov1 dataset with empty desc domain, might worth checking:

GLY_000612 SARS-CoV1 Glycosylation Sites (Literature) sarscov1_proteoform_glycosylation_sites_literature.csv

[CyrusAY]

$ python3 check-bco2filename-mapping.py | grep ERROR
NO-BCO,chicken_proteoform_glycosylation_sites_literature.csv,ERROR,in_fs
NO-BCO,rat_protein_citations_matrixdb.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_unicarbkb.csv,ERROR,in_fs
NO-BCO,rat_protein_matrixdb.csv,ERROR,in_fs

• chicken_proteoform_glycosylation_sites_literature.csv: see above comment
• chicken_proteoform_glycosylation_sites_unicarbkb.csv is not in the above list
• The BCO portal freezes whenever I try to access any bco domains of GLY_001038 | chicken_protein_participants_rhea.csv (edit: resolved itself)

[kmartinez834]

I have reviewed all of the new BCOs and created BCOs for rat_protein_matrixdb.csv and rat_protein_citations_matrixdb.csv. The remaining errors (chicken_proteoform_glycosylation_sites_literature.csv and chicken_proteoform_glycosylation_sites_unicarbkb.csv) are due to the presence of these files in unreviewed/ however the files are empty and were removed from the dataset-masterlist.json file.