O-Glycosylation predicted filter cannot be selected in beta.glygen.com

[ubhuiyan]

During my testing of the beta quick search for G17689DH, I filtered the search by "Disease" on the sidebar and noticed "N-Glycosylation predicted" and "O-Glycosylation predicted" popped up in the "By PTM" field.

It appears you can select "N-Glycosylation predicted", but not "O-Glycosylation predicted" despite there being one available result.

[rykahsay]

@sujeetvkulkarni ... can you tell me why the check box won't check? The API seems to be working (response shown at the bottom)

$ cat tests/temp/q.json 
{
        "id": "661b203ddf5c331146ae942fc2b28bbf",
        "offset": 1,
        "limit": 20,
        "order": "desc",
        "sort": "hit_score",
        "filters": [
            {
                "id": "by_data",
                "operator": "OR",
                "selected": [
                    "Disease"
                ]
            },
            {
                "id": "by_ptm",
                "operator": "OR",
                "selected": [
                    "O-Glycosylation predicted"
                ]
            }
        ]
    }

$ http POST :4442/protein/list/ < tests/temp/q.json 

HTTP/1.1 200 OK
Connection: close
Content-Length: 7299
Content-Type: application/json
Date: Wed, 28 Aug 2024 17:03:38 GMT
Server: gunicorn

{
    "cache_info": {
        "query": {
            "glytoucan_ac": "G17689DH",
            "organism": {
                "id": 9606,
                "name": "Human"
            }
        },
        "record_type": "protein",
        "search_type": "glycan_to_biosynthesis_enzymes",
        "ts": "2024-05-25 16:45:01 EDT-0400"
    },
    "filters": {
        "applied": [
            {
                "id": "by_data",
                "operator": "OR",
                "selected": [
                    "Disease"
                ]
            },
            {
                "id": "by_ptm",
                "operator": "OR",
                "selected": [
                    "O-Glycosylation predicted"
                ]
            }
        ],
        "available": [
            {
                "id": "by_mass",
                "label": "By Mass",
                "options": [
                    {
                        "count": 0,
                        "id": "0k_100k",
                        "label": "< 100K",
                        "order": 1
                    },
                    {
                        "count": 1,
                        "id": "100k_300k",
                        "label": "100K - 300K",
                        "order": 2
                    }
                ],
                "order": 4,
                "tooltip": ""
            },
            {
                "id": "by_organism",
                "label": "By Organism",
                "options": [
                    {
                        "count": 1,
                        "id": "Human",
                        "label": "Human",
                        "order": 1
                    }
                ],
                "order": 2,
                "tooltip": ""
            },
            {
                "id": "by_ptm",
                "label": "By PTM",
                "options": [
                    {
                        "count": 0,
                        "id": "N-Glycosylation reported",
                        "label": "N-Glycosylation reported",
                        "order": 1
                    },
                    {
                        "count": 1,
                        "id": "O-Glycosylation reported",
                        "label": "O-Glycosylation reported",
                        "order": 2
                    },
                    {
                        "count": 0,
                        "id": "N-Glycosylation predicted",
                        "label": "N-Glycosylation predicted",
                        "order": 3
                    },
                    {
                        "count": 1,
                        "id": "O-Glycosylation predicted",
                        "label": "O-Glycosylation predicted",
                        "order": 4
                    },
                    {
                        "count": 1,
                        "id": "Phosphorylation reported",
                        "label": "Phosphorylation reported",
                        "order": 5
                    }
                ],
                "order": 1,
                "tooltip": ""
            },
            {
                "id": "by_data",
                "label": "By Data",
                "options": [
                    {
                        "count": 1,
                        "id": "Mutagenesis",
                        "label": "Mutagenesis",
                        "order": 1
                    },
                    {
                        "count": 0,
                        "id": "SNV",
                        "label": "SNV",
                        "order": 2
                    },
                    {
                        "count": 1,
                        "id": "Pathway",
                        "label": "Pathway",
                        "order": 3
                    },
                    {
                        "count": 1,
                        "id": "Disease",
                        "label": "Disease",
                        "order": 4
                    },
                    {
                        "count": 1,
                        "id": "Publication",
                        "label": "Publication",
                        "order": 7
                    }
                ],
                "order": 3,
                "tooltip": ""
            },
            {
                "id": "by_biomarker_type",
                "label": "By Biomarker Type",
                "options": [],
                "order": 4,
                "tooltip": ""
            }
        ]
    },
    "pagination": {
        "limit": 20,
        "offset": 1,
        "order": "desc",
        "sort": "hit_score",
        "total_length": 1
    },
    "results": [
        {
            "biomarker_type": "",
            "disease": "developmental and epileptic encephalopathy 36 (Disease Ontology:DOID:0080470)",
            "function": "A female patient heterozygous for ALG13 Asn107Ser variant presented with infantile spasms, developmental delay, and dysmorphic features.  The patient showed normal pattern of glycosylated transferrin and random pattern of X-inactivation. Review article, [RefSeq, PubMed]; ALG13 X-linked intellectual disability: New variants, glycosylation analysis, and expanded phenotypes., [RefSeq, PubMed]; ALG13 and ALG14 form a functional endoplasmic reticulum UDP-N-acetylglucosamine transferase, [RefSeq, PubMed]; Catalytic subunit of the UDP-N-acetylglucosamine transferase complex that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation. The assembly of dolichol-linked oligosaccharides begins on the cytosolic side of the endoplasmic reticulum membrane and finishes in its lumen. The sequential addition of sugars to dolichol pyrophosphate produces dolichol-linked oligosaccharides containing fourteen sugars, including two GlcNAcs, nine mannoses and three glucoses. Once assembled, the oligosaccharide is transferred from the lipid to nascent proteins by oligosaccharyltransferases. On the cytoplasmic face of the endoplasmic reticulum, the dimeric ALG13/ALG14 complex catalyzes the second step of dolichol pyrophosphate biosynthesis, transferring a beta1,4-linked N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to GlcNAc-pyrophosphatedolichol (Gn-PDol) to produce N,N'-diacetylchitobiosyl diphosphodolichol. N,N'-diacetylchitobiosyl diphosphodolichol is a substrate for ALG1, the following enzyme in the biosynthetic pathway., [UniProtKB, PubMed, PubMed, PubMed]; Expanding the phenotype, genotype and biochemical knowledge of ALG3-CDG., [RefSeq, PubMed]; No glycosyltransferase or deubiquitinase activity is detected for this potential multifunctional enzyme., [UniProtKB, PubMed, PubMed]; The phenotypic spectrum of X-linked, infantile onset ALG13-related developmental and epileptic encephalopathy., [RefSeq, PubMed]; The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]., [RefSeq]; X-Linked ALG13 Gene Variant as a Cause of Epileptic Encephalopathy in Girls., [RefSeq, PubMed]",
            "gene_name": "ALG13",
            "gene_names_refseq": "ALG13; CDG1S; CXorf45; DEE36; EIEE36; GLT28D1; MDS031; TDRD13; YGL047W",
            "gene_names_uniprotkb": "ALG13; CXorf45; GLT28D1; MDS031",
            "hit_score": 20.54,
            "mass": 126056.0,
            "missing_score": 10000,
            "organism": "Human",
            "pathway": " (hsa:79868); Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein (R-HSA-446193); Defective ALG14 causes ALG14-CMS (R-HSA-5633231)",
            "predicted_glycosites": 1,
            "predicted_n_glycosites": 0,
            "predicted_o_glycosites": 1,
            "protein_name": "UDP-N-acetylglucosamine transferase subunit ALG13",
            "protein_names_refseq": "UDP-N-acetylglucosamine transferase subunit ALG13 isoform 3; hematopoietic stem/progenitor cells protein MDS031; UDP-N-acetylglucosamine transferase subunit ALG13 homolog; glycosyltransferase 28 domain-containing protein 1; tudor domain containing 13; asparagine-linked glycosylation 13 homolog; N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase; putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13",
            "protein_names_uniprotkb": "UDP-N-acetylglucosamine transferase subunit ALG13; 2.4.1.141; Asparagine-linked glycosylation 13 homolog; Glycosyltransferase 28 domain-containing protein 1",
            "publication_count": 41,
            "record_type": "protein",
            "refseq_ac": "NP_001034299",
            "refseq_name": "UDP-N-acetylglucosamine transferase subunit ALG13 isoform 3",
            "reported_fully_resolved_glycans": 1,
            "reported_glycation": 0,
            "reported_interactions": 0,
            "reported_mutagensis": 3,
            "reported_n_glycosites": 0,
            "reported_n_glycosites_with_glycan": 0,
            "reported_o_glycosites": 0,
            "reported_o_glycosites_with_glycan": 1,
            "reported_phosphosites": 6,
            "reported_snv": 0,
            "score_info": {
                "contributions": [
                    {
                        "c": "protein_exact_match",
                        "f": 0.0,
                        "w": 0.0
                    },
                    {
                        "c": "protein_top_glycan_definition_score",
                        "f": 0.0,
                        "w": 0.0
                    },
                    {
                        "c": "protein_reported_fully_resolved_glycans",
                        "f": 1.0,
                        "w": 10.0
                    },
                    {
                        "c": "protein_reported_n_glycosites_with_glycan",
                        "f": 0.0,
                        "w": 0.0
                    },
                    {
                        "c": "protein_reported_o_glycosites_with_glycan",
                        "f": 1.0,
                        "w": 5.0
                    },
                    {
                        "c": "protein_reported_n_glycosites",
                        "f": 0.0,
                        "w": 0.0
                    },
                    {
                        "c": "protein_reported_o_glycosites",
                        "f": 0.0,
                        "w": 0.0
                    },
                    {
                        "c": "protein_predicted_glycosites",
                        "f": 1.0,
                        "w": 3.0
                    },
                    {
                        "c": "protein_publication_count",
                        "f": 41.0,
                        "w": 2.0
                    }
                ],
                "formula": "sum(w + 0.01*f)",
                "variables": {
                    "c": "condition name",
                    "f": "condition match frequency",
                    "w": "condition weight"
                }
            },
            "tax_id": 9606,
            "total_n_glycosites": 0,
            "total_o_glycosites": 2,
            "total_reported_n_glycosites": 0,
            "total_reported_o_glycosites": 1,
            "uniprot_canonical_ac": "Q9NP73-1"
        }
    ]
}

[sujeetvkulkarni]

@rykahsay Ideally this new filter should not appear in first place after selecting disease. As after user selecting a filter options or data needs to be reduced not increased.

intial list request does not send the filter https://beta-api.glygen.org/protein/list?query={"id":"661b203ddf5c331146ae942fc2b28bbf","offset":1,"limit":20,"order":"desc","sort":"hit_score","filters":[]}

response:

{
                "id": "by_ptm",
                "label": "By PTM",
                "order": 1,
                "tooltip": "",
                "options": [
                    {
                        "id": "N-Glycosylation reported",
                        "label": "N-Glycosylation reported",
                        "count": 6,
                        "order": 1
                    },
                    {
                        "id": "O-Glycosylation reported",
                        "label": "O-Glycosylation reported",
                        "count": 11,
                        "order": 2
                    },
                    {
                        "id": "N-Glycosylation predicted",
                        "label": "N-Glycosylation predicted",
                        "count": 6,
                        "order": 3
                    },
                    {
                        "id": "Phosphorylation reported",
                        "label": "Phosphorylation reported",
                        "count": 14,
                        "order": 5
                    }
                ]
            },

After user selects disease filter https://beta-api.glygen.org/protein/list?query={"id":"661b203ddf5c331146ae942fc2b28bbf","offset":1,"limit":20,"order":"desc","sort":"hit_score","filters":[{"id":"by_data","operator":"OR","selected":["Disease"]}]}

"O-Glycosylation predicted" filter appears

response:

{
                "id": "by_ptm",
                "label": "By PTM",
                "order": 1,
                "tooltip": "",
                "options": [
                    {
                        "id": "N-Glycosylation reported",
                        "label": "N-Glycosylation reported",
                        "count": 3,
                        "order": 1
                    },
                    {
                        "id": "O-Glycosylation reported",
                        "label": "O-Glycosylation reported",
                        "count": 8,
                        "order": 2
                    },
                    {
                        "id": "N-Glycosylation predicted",
                        "label": "N-Glycosylation predicted",
                        "count": 3,
                        "order": 3
                    },
                    {
                        "id": "O-Glycosylation predicted",
                        "label": "O-Glycosylation predicted",
                        "count": 1,
                        "order": 4
                    },
                    {
                        "id": "Phosphorylation reported",
                        "label": "Phosphorylation reported",
                        "count": 9,
                        "order": 5
                    }
                ]
            },

"O-Glycosylation predicted" filter should not appear in first place (after user selects disease filter) as there was no associated data related to ti in original request.

I will look into why it is not getting selected but a new filter should not appear after user selects a filter as data should reduce not increase after filter selection.

[rykahsay]

@ubhuiyan It is fixed now, please check it

[ubhuiyan]

Looks good.