Issues

• Built-in full-text retrieval from publisher text-mining APIs (Elsevier, Springer Nature)

  neurostuff/autonima#83 · Filter by author adelavega opened on Sep 28, 2026

• Criteria IDs are numbered across both screening stages, so adding an abstract criterion relabels cached full-text decisions

  neurostuff/autonima#81 · Filter by author adelavega opened on Sep 28, 2026

• Config fields that validate but do nothing, and a full_text_sources validation rule that never runs

  neurostuff/autonima#80 · Filter by author adelavega opened on Sep 28, 2026

• this branch of pubget should be used in order to keep access to demographic tables/other important information in the extracted text.

  neurostuff/autonima#74 · Filter by author jdkent opened on Sep 16, 2026

• ASRreview inspiration

  neurostuff/autonima#71 · Filter by author jdkent opened on Sep 8, 2026

• Abstract screening: output is 88% of the stage's cost, and it is all written justification

  neurostuff/autonima#69 · Filter by author adelavega opened on Sep 4, 2026

• Prompts put varying content before invariant content, so prefix caching almost never hits (1.7% on full-text screening)

  neurostuff/autonima#68 · Filter by author adelavega opened on Sep 4, 2026

• Screening and annotation send the bibliography to the model: ~35% of input is never used

  neurostuff/autonima#67 · Filter by author adelavega opened on Sep 4, 2026

• One failing full_text_source silently discards all the others (99% corpus loss from a missing optional dependency)

  neurostuff/autonima#66 · Filter by author adelavega opened on Sep 3, 2026

• Unresolvable table_id aborts the whole run instead of degrading one analysis's metadata

  neurostuff/autonima#65 · Filter by author adelavega opened on Sep 3, 2026

• No record of what changed between config versions: derive a semantic version diff in the UI

  neurostuff/autonima#64 · Filter by author adelavega opened on Sep 3, 2026

• synthscholar

  neurostuff/autonima#63 · Filter by author jdkent opened on Sep 2, 2026

• Sparse analysis names: 2.6% of analyses are unnamed AND 74% of those have no description, so annotation has nothing to judge from

  neurostuff/autonima#61 · Filter by author adelavega opened on Aug 30, 2026

• Duplicate coordinate tables reach the meta-analysis: ~30% of papers carry re-ingested tables, silently double-weighting studies

  neurostuff/autonima#60 · Filter by author adelavega opened on Aug 30, 2026

• annotation metadata_fields has two different defaults depending on construction path (study_fulltext included or not)

  neurostuff/autonima#59 · Filter by author adelavega opened on Aug 27, 2026

• Unknown config keys are silently dropped in annotation/screening/retrieval and at top level (but rejected in search/output)

  neurostuff/autonima#58 · Filter by author adelavega opened on Aug 27, 2026

• search: query and pmids_file are silently unioned, but the docstring says query is ignored

  neurostuff/autonima#57 · Filter by author adelavega opened on Aug 27, 2026
  1

• PubMed abstracts truncated to first section; titles cut at inline markup; MeSH never collected

  neurostuff/autonima#56 · Filter by author adelavega opened on Aug 26, 2026

• Add a machine-readable provenance field to configs (what changed, who changed it, informed by what)

  neurostuff/autonima#55 · Filter by author adelavega opened on Aug 26, 2026

• No token/cost accounting: per-stage API cost cannot be reconstructed from run outputs

  neurostuff/autonima#54 · Filter by author adelavega opened on Aug 26, 2026

• PubMed search silently truncates at 10,000 results; max_results above that is ignored

  neurostuff/autonima#53 · Filter by author adelavega opened on Aug 26, 2026

• Idea: Enable local models

  neurostuff/autonima#52 · Filter by author adelavega opened on Aug 25, 2026

• UI Ideas

  neurostuff/autonima#48 · Filter by author adelavega opened on May 20, 2026

• IDEA: Auto-extract concepts, definitions, tasks for discovery

  neurostuff/autonima#46 · Filter by author adelavega opened on May 7, 2026

• Compare neurostore-text-extractor with autonima

  neurostuff/autonima#45 · Filter by author jdkent opened on Apr 27, 2026