Advanced Usage

Interactive Disambiguation

When OneCite finds multiple potential matches for a reference, it can enter interactive mode to let you choose the correct one.

Enabling Interactive Mode

onecite process ambiguous.txt --interactive

Example Session

Processing ambiguous.txt...

Found 2 matches for "Deep learning Hinton":

1. Deep Learning
   Authors: Yann LeCun, Yoshua Bengio, Geoffrey Hinton
   Journal: Nature
   Year: 2015
   Volume: 521, Pages: 436-444
   DOI: 10.1038/nature14539

2. Deep Belief Networks
   Authors: Geoffrey E. Hinton, Simon Osindero, Yee-Whye Teh
   Journal: Neural Computation
   Year: 2006
   Volume: 18, Pages: 1527-1554
   DOI: 10.1162/neco.2006.18.7.1527

Please select (1-2, 0=skip): 1
✅ Selected: Deep Learning (10.1038/nature14539)

Batch Processing Multiple Files

Process multiple files sequentially:

for file in *.txt; do
    onecite process "$file" -o "${file%.txt}.bib"
done

Working with Different Data Sources

OneCite intelligently routes queries to appropriate data sources:

For Biomedical Literature

Add search terms related to medicine, biology, or health:

onecite process medical_refs.txt

This will prioritize PubMed when available.

For Computer Science

Add search terms related to CS topics:

onecite process cs_refs.txt

This will prioritize DBLP and arXiv.

For General Academic Work

Mixed references will use CrossRef and Semantic Scholar:

onecite process general_refs.txt

Custom Templates

OneCite uses YAML-based templates for output formatting. See Custom Templates for detailed information.

Working with Large Reference Lists

For large files (100+ entries), use quiet mode to improve performance:

onecite process large_file.txt --quiet -o output.bib

Memory-Efficient Processing

OneCite processes references sequentially, so it should handle files with thousands of entries. If you encounter memory issues, split your input file:

# Split into chunks
split -l 100 large_file.txt chunk_

# Process each chunk
for chunk in chunk_*; do
    onecite process "$chunk" -o "${chunk}.bib"
done

Error Handling and Recovery

Handling Failed Entries

If OneCite cannot process a reference, it will skip it and continue. Check the output for warnings.

To debug specific entries, process them individually:

echo "your_reference_here" > test.txt
onecite process test.txt

Combining Results

To merge multiple .bib files:

cat file1.bib file2.bib file3.bib > combined.bib

Converting Between Formats

Convert BibTeX to APA:

onecite process input.bib --output-format apa -o output.txt

Convert APA to BibTeX:

# First save APA format in a parseable way, then convert back
onecite process references.txt --output-format apa -o apa_refs.txt
# Then process again to get BibTeX
onecite process original.txt -o output.bib

Using with Git for Version Control

Track changes to your bibliography:

git add references.txt results.bib
git commit -m "Update bibliography with new papers"

This allows you to see exactly what changed in your citations over time.

Integration with LaTeX and Overleaf

  1. Export your references to a .bib file:

    onecite process references.txt -o my_references.bib

  2. In your LaTeX file, add:

    \bibliography{my_references}
\bibliographystyle{plain}

  3. Upload to Overleaf and you’re done!

Python API Advanced Usage

For advanced Python usage, see Python API Reference.

Next Steps