Use this tool to analyze GFF files for PFAM domains and show genomic locations. Use AFTER get_samples_by_annotation to get the actual gene coordinates and genomic context. Takes a data_object_id from the previous search results and downloads the entire GFF file by default to show specific gene annotations containing the PFAM domains. Only use sample_bytes parameter if you specifically need to limit download size.

Use this tool to find biosamples that contain specific PFAM protein domains. Returns structured data about biosamples, their activities, and data objects. Perfect for finding samples with particular functional capabilities.

Use this tool to discover what types of data are available in the NMDC database. Returns a list of collection names like 'biosample_set', 'study_set', etc.

Use this tool to get statistics about NMDC collections including document counts. Helps understand the size and scope of available data.

Use this tool to get lists of IDs from NMDC collections in batches. Useful for sampling or systematic analysis of large datasets.

Use this tool to find biosamples collected within a specific elevation range. Perfect for studying altitude-related microbial communities.

Use this tool to find biosamples collected within a specific geographic bounding box defined by latitude and longitude coordinates.

Use this tool to find biosamples from specific ecosystem types, categories, or subtypes. Perfect for studying particular environments like soil, marine, or host-associated microbiomes.

Use this tool to retrieve any NMDC entity by its ID. Works with biosamples, studies, data objects, and other NMDC entities.

Use this tool to retrieve specific fields from an NMDC entity by ID. More efficient than getting full entities when you only need certain fields.

Use this tool to retrieve specific fields from multiple NMDC entities by their IDs. Efficient for batch operations with field filtering.

Use this tool to find the study associated with a specific biosample. Returns study information and metadata.

Use this tool to find all biosamples associated with a specific study. Returns a list of biosample IDs and metadata.

Use this tool to get detailed DOI information for a study, including publication DOIs, dataset DOIs, and award DOIs.

Use this tool to search for studies based on DOI criteria like provider, category, or DOI value patterns. Perfect for finding published studies or datasets from specific sources.

Use this tool to find biosamples with specific functional annotations. Returns COMPLETE biosample records including all data objects (GFF files, protein files, etc.) with their IDs and URLs. ALWAYS set max_records to match the user's request (e.g., if they ask for '1 sample' or 'a sample', set max_records=1). Use max_records, NOT limit, to control how many samples to return. Required formats: PFAM domains use 'PFAM:PF04183', KEGG use 'KEGG.ORTHOLOGY:K00001', COG use 'COG:COG0001', GO use 'GO:GO0000001'. When users want genomic locations of domains, use this first to find samples, then use fetch_and_filter_gff_by_pfam_domains with a GFF data_object_id from the results.