8000 How to convert .sbgn glyph ids to protein Identifiers · Issue #15 · reactome/content-service · GitHub
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How to convert .sbgn glyph ids to protein Identifiers #15

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nvelden opened this issue Jun 30, 2023 · 0 comments
Open

How to convert .sbgn glyph ids to protein Identifiers #15

nvelden opened this issue Jun 30, 2023 · 0 comments

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@nvelden
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nvelden commented Jun 30, 2023

I downloaded the SBGN file for pathway R-HSA-400511 from the reactome website. Is there anyway that I can convert the glyph id to there associated protein or compound id?

....
 <glyph class="process" id="reactionVertex_400459_16">
            <label text="Signal peptidase hydrolyzes preproGLP-1 to proGLP-1"/>
            <bbox w="12.0" h="12.0" x="316.0" y="297.0"/>
            <port id="reactionVertex_400459.1" x="321.0" y="313.0"/>
            <port id="reactionVertex_400459.2" x="322.0" y="293.0"/>
        </glyph>
        <glyph class="simple chemical" id="entityVertex_70115_38">
            <label text="Glc"/>
            <bbox w="35.0" h="30.0" x="18.0" y="878.0"/>
        </glyph>
        <glyph class="complex" id="entityVertex_264960_18">
            <label text="Signal Peptidase"/>
            <bbox w="125.0" h="24.0" x="459.0" y="244.0"/>
        </glyph>
        <glyph class="omitted process" id="reactionVertex_400509_42">
            <label text="Glucose-dependent Insulinotropic Polypeptide is secreted from intestinal K cells"/>
            <bbox w="12.0" h="12.0" x="762.0" y="780.0"/>
            <port id="reactionVertex_400509.1" x="767.0" y="796.0"/>
            <port id="reactionVertex_400509.2" x="768.0" y="776.0"/>
        </glyph>
....

pathwayCommons offers a mapping table with each glyph id and their associated uniprot id. Is there anything like this for Reactome?

 Uniprot                                                                     pathwayCommons
1  325053920   http://pathwaycommons.org/pc12/Protein_intact_EBI-8580945_identity_1568340696910
2 A0A024QZJ7 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZJ7_identity_1568341662043
3 A0A024QZJ7 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZJ7_identity_1568341663929
4 A0A024QZN9 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZN9_identity_1568341660942
5 A0A024QZN9 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZN9_identity_1568341663069
6 A0A024QZR3 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZR3_identity_1568341661337
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