literature

literature

When to use

Extract GEO accessions and heuristic study metadata from paper text. Read local papers explicitly with read_document or fetch remote papers with fetch_text. Skip when the dataset is already in hand.

Use from a step

import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill('literature')
text = read_input('paper.txt', reader=library.read_document)
result = library.extract(text)
write_output(result, 'tables/result.csv')

examples/example_step.py runs offline and supports fresh-kernel replay. Pure computations return objects; CLI and steps own writes.

API

extract(data)

Extract GEO accessions and heuristic study metadata from text.

:param data: Local paper text; URLs and paths are treated as text, never fetched. :returns: A DataFrame of kind/accession pairs, with metadata in attrs['run_info']. :raises ValueError: data is empty or not a string.

methodology(data)

Extract stated numeric method parameters with exact source spans.

:param data: Paper text containing supported parameter names and numeric values. :returns: A DataFrame with param, operator, value, quote, start and end columns. :raises TypeError: data is not text.

read_document(data)

Read a local PDF or UTF-8 text file; use as reader= in read_input.

:param data: Local Path or path string; no network requests are made. :returns: Extracted text with empty PDF pages omitted. :raises ImportError: Install pypdf with install_skill_deps for PDFs. :raises OSError: The file cannot be read.

fetch_text(data, *, input_type='url')

Fetch article text explicitly from a URL, DOI or PubMed reference.

:param data: Reference sent to the remote service; results may change between requests. :param input_type: Default url; doi and pubmed resolve their respective endpoints. :returns: HTML/XML with tags removed and whitespace collapsed, as in the CLI. :raises ImportError: Install requests with install_skill_deps if unavailable. :raises ValueError: The reference type or URL scheme is unsupported. :raises Exception: HTTP and network errors propagate instead of becoming article text.