ioannis.foufoulas
/
openaire-graph-docs
forked from D-Net/openaire-graph-docs
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

added mapping uniprot/swiss

This commit is contained in:
Sandro La Bruzzo 2023-03-09 14:21:55 +01:00
parent da45601f2c
commit 49fc73d09d
1 changed files with 32 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

32
docs/data-provision/aggregation/non-compatible-sources/uniprot.md Normal file
View File

@ -0,0 +1,32 @@
# UniProtKB/Swiss-Prot
this section describes the mapping implemented for [UniProtKB/Swiss-Prot](https://www.uniprot.org/).
The whole dump can be downloaded by [here](https://www.uniprot.org/help/downloadss) the Reviewed (Swiss-Prot).
From this Dump we extract only the protein linked to a pubmed Publication.
## Entity Mapping
The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph dump format.
You can check an example of the text metadata [here](https://rest.uniprot.org/uniprotkb/A0A0C5B5G6.txt)
| OpenAIRE Result field path | FASTA record field xpath| Notes|
|--------------------------------|----------------------|---------|
| **BIOEntity Mapping** | | |
| `id` | `LINE Starts with AC` | id in the form `uniprot_____::md5(id)`|
| `pid` | `LINE Starts with AC` | example `AC A0A0C5B5G6;` classid=classname=`uniprot` the vaue is the text after `AC` |
| `publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be `YYYY-mm-dd` |
| `maintitle` | `LINE START WITH GN`|main title |
| **Instance Mapping** | | |
| `instance.type` | | `Bioentity` |
| `type` | | `Dataset` |
| `instance.pid` | `LINE Starts with AC` | `classid = classname = uniprot` |
| `instance.url` | `pid` | prepend to the value `https://www.uniprot.org/uniprot/`|
| `instance.publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be YYYY-mm-dd |
### Relation Mapping
| OpenAIRE Relation Semantic and inverse | Source/Target type | Notes |
|----------------------------------------|---------------------|--------------------------------------------------------------------------|
| `IsRelatedTo` | `LINE START WITH RX` | we create relationships between the BioEntity and the pubmed or DOI generating an unresolved target identifier |