Batch retrieval tool: Difference between revisions
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GlyGen is developing a new tool in 2.9 (release at the end of August 2025) that allows enriching tables of proteins/genes with additional information derived from GlyGen. The tool will map user provided protein identifiers ( | GlyGen is developing a new tool in 2.9 (release at the end of August 2025) that allows enriching tables of proteins/genes with additional information derived from GlyGen. The tool will map user provided protein identifiers (UniProtKB Accession, Protein Names, RefSeq ID, and Gene symbol) with canonical protein accession and add user requested information in the form of additional columns to these identifiers. The generated table can be downloaded as an Excel like file and can be used to merge the additional information into an existing data table. As an example, this can be used to enrich protein tables generated by mass spec software tools with additional information to help interpret and preprocess the data. e.g., by adding columns that identify the location of the protein (subcellular, membrane-bound) or the functional classification of proteins (kinases, transporters ...). | ||
Please see annotation examples below: | |||
1. | 1. Annotate UniProtKB Accession list with GO Name -> membrane. | ||
<div style=display:inline-grid> | <div style=display:inline-grid> | ||
{| class="wikitable" | {| class="wikitable" | ||
|+ Input | |+ Input List | ||
|- | |- | ||
! | ! UniProtKB Accession | ||
|- | |- | ||
| Q8NE71 | | Q8NE71 | ||
|- | |- | ||
| O60220-1 | | O60220-1 | ||
| Line 17: | Line 17: | ||
| Q9NX14-1 | | Q9NX14-1 | ||
|- | |- | ||
| Q14699 | | Q14699 | ||
|- | |- | ||
| | | Q86UP2-1 | ||
|- | |- | ||
| | | Q96EK5-1 | ||
|- | |- | ||
| P55058-1 | | P55058-1 | ||
|- | |||
| XYZXX-1 | |||
|} | |} | ||
</div> | </div> | ||
| Line 35: | Line 37: | ||
|+ Output Table | |+ Output Table | ||
|- | |- | ||
! | ! UniProtKB Accession | ||
! UniProtKB Mapping | |||
! GO Name | ! GO Name | ||
|- | |- | ||
| Q8NE71-1 | | Q8NE71-1 | ||
| Yes | |||
| membrane | | membrane | ||
|- | |- | ||
| O60220-1 | | O60220-1 | ||
| Yes | |||
| membrane | | membrane | ||
|- | |- | ||
| Q9NX14-1 | | Q9NX14-1 | ||
| Yes | |||
| membrane | | membrane | ||
|- | |- | ||
| Q14699-1 | | Q14699-1 | ||
| Yes | |||
| membrane | | membrane | ||
|- | |- | ||
| | | Q86UP2-1 | ||
| Yes | |||
| membrane | | membrane | ||
|- | |||
| Q96EK5-1 | |||
| Yes | |||
| | |||
|- | |||
| P55058-1 | |||
| Yes | |||
| | |||
|- | |||
| XYZXX-1 | |||
| NOT FOUND | |||
| | |||
|} | |||
</div> | |||
2. Annotate UniProtKB Accession list with GO ID -> GO:0016020. | |||
<div style=display:inline-grid> | |||
{| class="wikitable" | |||
|+ Input List | |||
|- | |||
! UniProtKB Accession | |||
|- | |||
| Q86UP2-1 | |||
|- | |||
| P08575-3 | |||
|- | |||
| Q13308-1 | |||
|- | |||
| O95196-1 | |||
|- | |||
| Q8NC56-1 | |||
|- | |||
| K7GQZ4-1 | |||
|- | |||
| P55058-1 | |||
|} | |||
</div> | |||
<div style="display:inline-grid"> | |||
{| style="vertical-align:center" | |||
| ⇒ | |||
|} | |||
</div> | |||
<div style=display:inline-grid> | |||
{| class="wikitable" | |||
|+ Output Table | |||
|- | |||
! UniProtKB Accession | |||
! UniProtKB Mapping | |||
! GO ID | |||
|- | |||
| Q86UP2-1 | |||
| Yes | |||
| GO:0016020 | |||
|- | |||
| P08575-3 | |||
| Yes | |||
| GO:0016020 | |||
|- | |||
| Q13308-1 | |||
| Yes | |||
| GO:0016020 | |||
|- | |||
| O95196-1 | |||
| Yes | |||
| GO:0016020 | |||
|- | |||
| Q8NC56-1 | |||
| Yes | |||
| GO:0016020 | |||
|- | |- | ||
| K7GQZ4-1 | | K7GQZ4-1 | ||
| | | Yes | ||
| | |||
|- | |- | ||
| P55058-1 | | P55058-1 | ||
| | | Yes | ||
| | |||
|} | |} | ||
</div> | </div> | ||
Latest revision as of 22:22, 9 May 2025
GlyGen is developing a new tool in 2.9 (release at the end of August 2025) that allows enriching tables of proteins/genes with additional information derived from GlyGen. The tool will map user provided protein identifiers (UniProtKB Accession, Protein Names, RefSeq ID, and Gene symbol) with canonical protein accession and add user requested information in the form of additional columns to these identifiers. The generated table can be downloaded as an Excel like file and can be used to merge the additional information into an existing data table. As an example, this can be used to enrich protein tables generated by mass spec software tools with additional information to help interpret and preprocess the data. e.g., by adding columns that identify the location of the protein (subcellular, membrane-bound) or the functional classification of proteins (kinases, transporters ...).
Please see annotation examples below:
1. Annotate UniProtKB Accession list with GO Name -> membrane.
| UniProtKB Accession |
|---|
| Q8NE71 |
| O60220-1 |
| Q9NX14-1 |
| Q14699 |
| Q86UP2-1 |
| Q96EK5-1 |
| P55058-1 |
| XYZXX-1 |
| ⇒ |
| UniProtKB Accession | UniProtKB Mapping | GO Name |
|---|---|---|
| Q8NE71-1 | Yes | membrane |
| O60220-1 | Yes | membrane |
| Q9NX14-1 | Yes | membrane |
| Q14699-1 | Yes | membrane |
| Q86UP2-1 | Yes | membrane |
| Q96EK5-1 | Yes | |
| P55058-1 | Yes | |
| XYZXX-1 | NOT FOUND |
2. Annotate UniProtKB Accession list with GO ID -> GO:0016020.
| UniProtKB Accession |
|---|
| Q86UP2-1 |
| P08575-3 |
| Q13308-1 |
| O95196-1 |
| Q8NC56-1 |
| K7GQZ4-1 |
| P55058-1 |
| ⇒ |
| UniProtKB Accession | UniProtKB Mapping | GO ID |
|---|---|---|
| Q86UP2-1 | Yes | GO:0016020 |
| P08575-3 | Yes | GO:0016020 |
| Q13308-1 | Yes | GO:0016020 |
| O95196-1 | Yes | GO:0016020 |
| Q8NC56-1 | Yes | GO:0016020 |
| K7GQZ4-1 | Yes | |
| P55058-1 | Yes |