Article Keyword Search¶
This reference documents how -k/--keyword behaves and when to pair it with
typed article filters.
When --keyword should stand alone¶
Use keyword-only article search when the question does not start with a known gene, disease, or drug anchor.
- Unknown-entity questions: search the evidence first instead of inventing a
typed
-g,-d, or--drugvalue. - Dataset or method questions: keep the search free-text and add
--type reviewwhen you want synthesis papers or surveys.
Examples:
biomcp search article -k '"cafe-au-lait spots" neurofibromas disease' --type review --limit 5
biomcp search article -k "TCGA mutation analysis dataset" --type review --limit 5
On the default --source all route, adding -k/--keyword also brings LitSense2
into compatible federated searches and makes the default relevance mode
hybrid.
That semantic-aware path uses the LitSense2-derived semantic signal; rows
without LitSense2 provenance contribute semantic=0.
When --keyword should be combined with typed filters¶
If the gene, disease, or drug is already known, keep that anchor in a typed
flag and use -k for mechanisms, phenotypes, outcomes, datasets, and other
free-text concepts.
Example:
Without -k, typed-only searches stay on the compatible federated lexical
route.
Do not invent typed flags for unknown entities¶
If the question is "which disease causes this phenotype?" or "which drug causes
this effect?", do not guess a disease or drug name just to fill -d or
--drug. Start with keyword-only search, then rerun with a typed flag once the
first page reveals the likely anchor. If you need BioMCP to resolve the entity
before you search, use biomcp discover "<question>".
Keyword behavior¶
--keyword (-k) is treated as escaped free text and no longer auto-quotes
whitespace-containing values.
This allows multi-word keyword retrieval such as:
Phrase behavior for entity filters¶
Entity-oriented filters retain phrase quoting behavior:
--gene--disease--drug--author
Example:
Combined filters¶
Filters can also be combined with typed anchors and other article controls: