ebi-pdbe-search
Run raw Solr queries against the PDBe search index to filter, facet, group, sort, and paginate protein structure results using fielded criteria.
Instructions
Executes a search query against the PDBe Solr search service.
This tool exposes common Solr query parameters directly so users can construct fielded queries, filter queries, field lists, facets, grouping, sorting, and pagination against the PDBe search index.
IMPORTANT: query is passed to Solr as the raw q parameter. Use Solr query syntax such as *:*, pdb_id:1cbs, text:*kinase*, boolean clauses, ranges, and boosts as needed.
IMPORTANT: the text field is a copy field that contains the full searchable text aggregated from the document. Use text:*<term>* when you want a broad wildcard text search.
Expected Input Parameters:
- query (string): Raw Solr query string passed as q.
- fl (string or list of strings, optional): Solr field list. The legacy filters parameter is also accepted as an alias.
- filters (list of strings, optional): Backwards-compatible alias for fl.
- fq (string, object, list of strings, or list of objects, optional): Solr filter query or queries to narrow down the search results. Objects are converted to fielded filters, e.g. {"experimental_method": "X-ray diffraction"} becomes experimental_method:"X-ray diffraction".
- sort (string, optional): The sorting criteria for the search results.
- start (integer, optional): The starting index for pagination of results.
- rows (integer, optional): The number of results to return.
- facet (boolean, optional): Enable Solr faceting.
- facet_fields (string or list of strings, optional): Field facets, sent as facet.field.
- facet_queries (string or list of strings, optional): Query facets, sent as facet.query.
- facet_limit, facet_mincount, facet_sort (optional): Common facet controls.
- group (boolean, optional): Enable Solr grouping.
- group_field (string or list of strings, optional): Grouping field, sent as group.field.
- group_limit, group_offset, group_sort (optional): Common grouping controls.
- params (object, optional): Additional Solr parameters to pass through for advanced use.
Example Input:
{
"query": "text:*kinase*",
"fl": ["pdb_id", "title", "deposition_date"],
"fq": ["experimental_method:\"X-ray diffraction\""],
"facet": true,
"facet_fields": ["experimental_method"],
"sort": "deposition_date desc",
"start": 0,
"rows": 10
}
Expected Output Format:
A text representation of the search results, formatted in a readable manner. The output will include:
- Metadata about the search results (e.g. number of documents found, start index).
- A list of documents matching the search query, with each document's fields and values clearly presented.
The output will be structured to facilitate easy interpretation of the search results, allowing users to quickly identify relevant information.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| fl | No | ||
| fq | No | ||
| rows | No | ||
| sort | No | ||
| facet | No | ||
| group | No | ||
| query | Yes | ||
| start | No | ||
| params | No | ||
| filters | No | ||
| facet_sort | No | ||
| group_main | No | ||
| group_sort | No | ||
| facet_limit | No | ||
| group_field | No | ||
| group_limit | No | ||
| group_query | No | ||
| facet_fields | No | ||
| group_format | No | ||
| group_offset | No | ||
| facet_queries | No | ||
| group_ngroups | No | ||
| facet_mincount | No |