How to connect Amass MCP with DeepSeek Harness

Search publications in Amass BiomedCore — optimized for publication search. 43M+ PubMed/PMC citations with abstracts, fulltext, and cross-links to clinical trials (TrialCore), plus conference abstracts from society meetings, which carry `Conference` in `publicationTypes`. **Use when** finding peer-reviewed biomedical literature, systematic reviews, clinical evidence, drug mechanism studies or life science research, or the congress abstracts that report a trial readout before the full paper. For fetching a known PMID, DOI, or Amass Id directly, use `get_amass_biomedcore_record` instead.

Fetch a single publication by Amass Id, PMID, or DOI from Amass BiomedCore. Returns the full enriched record including abstract, fulltext where available, and cross-links to clinical trials (TrialCore). A record sourced from a conference abstract carries `Conference` in `publicationTypes`. **Use when** you already have an Amass Id, PMID, or DOI and need the complete record. For discovery by topic, author, journal, or other criteria, use `search_amass_biomedcore_records` instead.

Search clinical trials in Amass TrialCore — optimized for trial search. 1.2M+ trials from ClinicalTrials.gov and the WHO ICTRP (non-US registries such as EUCTR, ChiCTR, and JPRN). Each result carries the trial's summary, sponsor, phase, status and why it stopped (`whyStopped`), start and completion dates, enrollment (actual or estimated), conditions, interventions, countries, whether results were posted, and `registryId`, `sourceRegistry`, and `sourceUrl` identifying its source (non-US trials have a null `nctId`). For endpoints, arms, collaborators, posted results, and cross-links to publications and drugs, fetch the trial with `get_amass_trialcore_record`. **Use when** finding clinical trials by indication, sponsor, phase, or endpoint; competitive trial landscape analysis; identifying recruitment status and trial design patterns; assessing clinical development pipelines. A trial identifier in the query returns that trial first, whether an NCT Id or an ICTRP registry-native Id. A sponsor drug code in the query (NN9535, MK-3475, PF-06651600) returns the trials ahead of everything else, followed by the drug's other trials when the code resolves to a single drug. An EU trial registered in several countries appears once, as its best-matching country registration; to get every country's registration, call `get_amass_trialcore_record` with the EudraCT number minus its country suffix (EUCTR2018-002618-11). A trial registered with ClinicalTrials.gov and another registry appears once, preferring its ClinicalTrials.gov record, whose secondaryIds lists the other registrations. For fetching a known NCT Id, registry Id or Amass Id on its own, use `get_amass_trialcore_record` instead.

Fetch a single clinical trial by Amass Id, NCT Id, or registry Id from Amass TrialCore (ClinicalTrials.gov plus non-US trials from the WHO ICTRP). Returns the trial's summary, phase, status and why it stopped (`whyStopped`), dates, enrollment (actual or estimated), sponsor and collaborators, conditions, interventions and arms, registered primary and secondary endpoints, whether and when results were posted, source-registry provenance (`registryId`, `sourceRegistry`, `sourceUrl`), and cross-links to publications (BiomedCore) and drugs (DrugCore). Set `includeOutcomes` to also get the posted results. Non-US trials have a null `nctId` — fetch them by Amass Id or `registryId` (the source-registry native id, e.g. EUCTR/ChiCTR/JPRN). **Use when** you already have an Amass Id, NCT Id, or registry Id and need the trial's details. For discovery by indication, sponsor, phase, endpoint, or other criteria, use `search_amass_trialcore_records` instead.

Search regulatory authorizations in Amass RegulatoryCore — unified FDA + EMA regulatory data. Covers NDA/BLA authorizations, centralized EMA marketing authorizations, with cross-agency search by default. **Use when** finding drug approvals, marketing authorizations, regulatory status, orphan designations, or comparing FDA vs EMA approvals. For fetching a known Amass Id directly, use `get_amass_regulatorycore_record` instead.

Fetch a single regulatory authorization by Amass Id, FDA application number, EMA product number, NDC, or SPL Set ID from Amass RegulatoryCore. All five keys return the same record and the same fields, so there is no need to resolve one to an Amass Id first. Returns the full record with all harmonized fields including EMA and FDA details, plus `documentSections`: the record's table of contents over its parsed source documents (FDA labels/reviews, EMA SmPCs/EPARs), listing each section's docType, path and title. The TOC is structural, carrying no body text and no matchedText (that is search-only). Pass a documentSectionId to `get_amass_regulatorycore_document_section` for the section's full text. To look up by substance identity (INN, ATC, UNII, RxCUI), resolve through DrugCore and follow its referencesRegulatoryCore link. **Use when** you already have an identifier and need the complete record, or need to know which sections a product's source documents contain. An empty `documentSections` means Amass has parsed no source documents for that authorization. For discovery by topic or criteria, use `search_amass_regulatorycore_records` instead.

Fetch the full parsed text of one source-document section (FDA labels/reviews, EMA SmPCs/EPARs) from Amass RegulatoryCore by its Amass Id (AMRC_*) and document section id (AMRCDS_*). Returns the full section `content` plus metadata (docType, path, title, sourceUrl). The full source PDF is at the section's sourceUrl when the section can be tied to a single PDF; otherwise sourceUrl is null. **Use when** you have a documentSectionId from `search_amass_regulatorycore_records` (matchedText evidence excerpts) or from the table of contents on `get_amass_regulatorycore_record`, and you need the complete section body rather than just the excerpt.

Search drugs in Amass DrugCore — 22K+ harmonized drug/molecule records covering names, trade names, synonyms, modality, clinical stage, and chemical structure. **Use when** finding drugs by name or description, checking a drug's modality or clinical stage, or discovering candidates by keyword. For fetching a known Amass Id or ChEMBL Id directly, use `get_amass_drugcore_record` instead.

Fetch a single drug by Amass Id or ChEMBL Id from Amass DrugCore. Returns the full record with all harmonized fields including modality, clinical stage, chemical structure, parent/child relationships, and cross-links to clinical trials (TrialCore), literature (BioMedCore), regulatory authorizations (RegulatoryCore), and target genes (GeneCore). **Use when** you already have an identifier and need the complete record. For discovery by keyword or criteria, use `search_amass_drugcore_records` instead.

Search genes in Amass GeneCore — 43K+ harmonized gene records covering symbols, names, synonyms, gene families, gene type / biotype, NCBI RefSeq functional summary, genomic location, cross-references (Ensembl, Entrez, HGNC, UniProt, MANE, OMIM, Orphanet, IUPHAR), target intelligence (druggability/tractability, safety liabilities, target class, genetic constraint, CRISPR essentiality), and UniProt protein annotations (function, biophysics, structure/PTMs). **Use when** finding genes by symbol or name, discovering genes by functional concept (e.g. 'tyrosine kinase', 'GPCR', 'apoptosis'), checking a gene's biotype or location, or assessing drug targets by druggability, safety, target class or genetic constraint. For fetching a known Amass Id or Ensembl gene Id directly, use `get_amass_genecore_record` instead.

Fetch a single gene by Amass Id or Ensembl gene Id from Amass GeneCore. Returns the full record with all harmonized fields including gene type / biotype, NCBI RefSeq functional summary, gene family, genomic location, external identifiers (Entrez, HGNC, UniProt, MANE, OMIM, Orphanet, IUPHAR), target intelligence (tractability/druggability, safety liabilities, target class, genetic constraint, CRISPR essentiality), UniProt protein annotations (function, biophysics, structure/PTMs), and cross-links to drugs (DrugCore) that target the gene. **Use when** you already have an identifier and need the complete record. For discovery by keyword or criteria, use `search_amass_genecore_records` instead.

Search patents in Amass PatentCore (preview) — the life-science subset of the global patent corpus (USPTO, EPO, WIPO), served from Amass's own index. Full-text BM25 over title, abstract, claims, and description, with filters for jurisdiction, classification (CPC/IPC), assignee/inventor, dates, and forward-citation count. Records carry cross-links to DrugCore. **Use when** doing prior-art or freedom-to-operate searches, mapping a patent landscape, or finding patents by assignee, technology, or classification. For fetching a known publication number or Amass Id directly, use `get_amass_patentcore_record` instead.

Fetch a single patent by Amass Id or publication number from Amass PatentCore (preview). Returns the enriched record including bibliographic metadata, classifications (CPC/IPC), assignees/inventors, key dates, citation counts, and cross-links to DrugCore and BiomedCore records (Amass IDs). **Use when** you already have an Amass Id or publication number and need the record. For discovery by technology, assignee, or classification, use `search_amass_patentcore_records` instead.

Report a problem with data in an Amass Core (BiomedCore, TrialCore, DrugCore, GeneCore, RegulatoryCore, PatentCore). This is a write action: it stores a feedback report with Amass for the data team to review. It does not read or change any records, and it returns only a receipt (the report id and timestamp), not the report itself. **Optional.** Sending feedback is never required to answer a question or complete a task. Send it only when you have found a concrete data problem; do not send it to confirm that data looks fine. **Use when** you or the user notice a wrong, missing, outdated, or contradictory value in an Amass record (`DATA_QUALITY`); a search that missed or mis-ranked records that clearly exist (`DATA_QUALITY`, with `query` and `expectedIds`); or a question that cannot be answered because a field, filter, or cross-link does not exist (`DATA_MODEL`). **Only for Amass Core data.** Do not use it for web search results, other patent or literature databases, the assistant's own behaviour, or anything that did not come from an Amass Core tool. Name the affected Core(s) in `core`, and the record in `recordId` when the feedback concerns one record. **Write `message` so it stands on its own.** It is read without the conversation attached: state what was asked, what you expected, and what Amass actually returned, naming the concrete record ids, fields, and values. Do not refer to "the above", "this record", or anything else that only makes sense in context.