Extraction of species, genes and GO terms from publications, using GPT API
To use:
pip install -r requirements.txt
Get an openAI API key, from openAI.com
Save it in a text file called apikey.txt
python PubLLican.py <inputfile.pdf>
Output produced:
A summary of species, genes, and GO terms is printed to the console
.as.txt : a text representation of the pdf
.summary.txt : a text file summarising the publication
.genes.txt : a text list of possible gene names found in the pdf
.go.json the species, genes, and GO terms in machine-readable format
The cache folder stores the results of API requests, so that these are not repeated (potentially incurring costs) chatGPT is non-deterministic - the results you get may be different even with the same input
The following example is generated from the paper
"PI4-kinase and PfCDPK7 signaling regulate phospholipid biosynthesis in Plasmodium falciparum"
[https://pubmed.ncbi.nlm.nih.gov/34866326/]
PDF here: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8811644/pdf/EMBR-23-e54022.pdf]
| PubLLican Generated | Manually curated |
|---|---|
| Species: Plasmodium falciparum | Species: Plasmodium falciparum |
| Gene names | Gene Id (name) |
| EK | PF3D7_1124600 (EK) |
| PI4-kinase | PF3D7_1343000 (PMT) |
| PMT | PF3D7_1123100 (CDPK7) |
| PfCDPK7 | |
| PfPI4K | |
| GO terms | GO Terms: |
| GO:0006468 | GO:0006468 |
| GO:0006629 | GO:0006656 |
| GO:0008104 | GO:0005515 |
| GO:0008654 (Grandparent of GO:0006656 ) | GO:0004672 |
| GO:0006650 (Grandparent of GO:0006656 ) | |
| GO:0006644 (Parent of GO:0008654/GO:0006650) | |
| GO:0006631 |