TOOL_NAMES_REFERENCE.md

Literature Deep Research - Complete Tool Reference

All tool names for literature search + annotation databases used in enhanced research strategy.

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Literature Search Tools (18)

Biomedical & Life Sciences

'PubMed_search_articles'          # 35M+ papers - primary biomedical
'PMC_search_papers'               # Full-text biomedical archive (NIH)
'EuropePMC_search_articles'       # 42M+ European biomedical (use source='PPR' for preprints)
'BioRxiv_get_preprint'            # Get bioRxiv preprint by DOI (not search)
'MedRxiv_get_preprint'            # Get medRxiv preprint by DOI (not search)

Computer Science

'DBLP_search_publications'        # 6M+ CS publications
'ArXiv_search_papers'             # Physics/CS/math preprints
'SemanticScholar_search_papers'   # 200M+ AI-ranked papers

General Academic

'openalex_literature_search'      # 250M+ works across fields
'Crossref_search_works'           # 140M+ DOI registry
'Fatcat_search_scholar'           # Internet Archive
'DOAJ_search_articles'            # Open access journals

Regional/Specialized

'OpenAIRE_search_publications'    # EU-funded research
'HAL_search_archive'              # French national archive
'OSF_search_preprints'            # Social science preprints
'Zenodo_search_records'           # Datasets, software, publications

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Citation & Metadata Tools (7)

PubMed Citation Tools

'PubMed_get_article'              # Complete metadata for PMID
'PubMed_get_cited_by'             # Forward citations (papers citing this)
'PubMed_get_related'              # Computationally related papers
'PubMed_get_links'                # External links (full-text)

Europe PMC Citation Tools (Fallbacks)

'EuropePMC_get_citations'         # Forward citations (fallback for PubMed)
'EuropePMC_get_references'        # Backward citations (reference list)

Open Access

'Unpaywall_check_oa_status'       # OA status by DOI (requires email)

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Protein/Gene Annotation Tools (NEW in v5.0)

UniProt Tools

'UniProt_search'                  # Search UniProt by query
'UniProt_get_entry_by_accession'  # Full protein entry
'UniProt_id_mapping'              # Map between ID types
'UniProt_get_function_by_accession'  # Function description
'UniProt_get_sequence_by_accession'  # Protein sequence
'UniProt_get_recommended_name_by_accession'  # Official name
'UniProt_get_alternative_names_by_accession'  # Aliases
'UniProt_get_subcellular_location_by_accession'  # Localization
'UniProt_get_ptm_processing_by_accession'  # PTMs, active sites
'UniProt_get_disease_variants_by_accession'  # Disease variants

Domain/Structure Tools

'InterPro_get_protein_domains'    # Domain architecture
'alphafold_get_prediction'        # AlphaFold structure
'get_protein_metadata_by_pdb_id'  # PDB structure metadata
'proteins_api_get_protein'        # Alternative protein data

Gene Annotation

'MyGene_get_gene_annotation'      # NCBI gene info, aliases
'ensembl_lookup_gene'             # Ensembl gene details
'ensembl_get_xrefs'               # Cross-references

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Expression Tools (NEW in v5.0)

GTEx (Tissue Expression)

'GTEx_get_gene_expression'        # Expression data
'GTEx_get_median_gene_expression' # Median TPM by tissue

Human Protein Atlas

'HPA_get_comprehensive_gene_details_by_ensembl_id'  # Full HPA data
'HPA_get_rna_expression_by_source'  # RNA expression
'HPA_get_subcellular_location'    # Subcellular localization
'HPA_get_protein_interactions_by_gene'  # Interactions
'HPA_get_cancer_prognostics_by_gene'  # Cancer prognosis

Single-Cell (if available)

'CELLxGENE_get_expression_data'   # Single-cell expression

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Pathway & Function Tools (NEW in v5.0)

Gene Ontology

'GO_get_annotations_for_gene'     # GO terms (BP, MF, CC)
'GO_get_term_details'             # GO term details

Pathways

'Reactome_map_uniprot_to_pathways'  # Reactome pathways
'kegg_get_gene_info'              # KEGG gene/pathways
'WikiPathways_search'             # WikiPathways

Open Targets

'OpenTargets_get_target_gene_ontology_by_ensemblID'  # GO via OT
'OpenTargets_get_target_tractability_by_ensemblID'   # Druggability
'OpenTargets_get_associated_drugs_by_target_ensemblID'  # Known drugs
'OpenTargets_get_target_safety_profile_by_ensemblID'   # Safety
'OpenTargets_get_diseases_phenotypes_by_target_ensembl'  # Disease links
'OpenTargets_get_publications_by_target_ensemblID'   # Publications

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Interaction Tools

'STRING_get_protein_interactions'  # STRING PPI network
'intact_get_interactions'         # IntAct experimental PPIs
'intact_get_complex_details'      # Complex membership
'OpenTargets_get_target_interactions_by_ensemblID'  # OT interactions

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Variant & Disease Tools

gnomAD

'gnomad_get_gene'                 # Population variants
'gnomad_get_gene_constraints'     # Constraint scores (pLI, LOEUF)

ClinVar

'clinvar_search_variants'         # Clinical variants
'clinvar_get_variant_by_id'       # Variant details

Disease

'OpenTargets_get_diseases_phenotypes_by_target_ensembl'  # Disease associations
'DGIdb_get_drug_gene_interactions'  # Drug-gene
'DGIdb_get_gene_druggability'     # Druggability categories

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Tool Categories by Use Case

Target Disambiguation (Phase 1)

# Resolve IDs
'UniProt_search'
'UniProt_id_mapping'
'ensembl_lookup_gene'

# Get baseline profile
'InterPro_get_protein_domains'
'HPA_get_subcellular_location'
'GTEx_get_median_gene_expression'
'GO_get_annotations_for_gene'
'Reactome_map_uniprot_to_pathways'

High-Precision Literature Seeds

'PubMed_search_articles'          # "[GENE]"[Title] queries
'EuropePMC_search_articles'       # Alternative

Citation Network Expansion

'PubMed_get_cited_by'             # Forward citations (primary)
'EuropePMC_get_citations'         # Forward (fallback)
'PubMed_get_related'              # Related papers
'EuropePMC_get_references'        # Backward citations

Broad Search

'openalex_literature_search'      # Comprehensive
'Crossref_search_works'           # DOI-based
'SemanticScholar_search_papers'   # AI-ranked

OA Status Check

'Unpaywall_check_oa_status'       # If email provided
# Otherwise use OA fields from:
# - EuropePMC (isOpenAccess)
# - OpenAlex (is_oa)
# - PMC papers (all OA)

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Fallback Chains

Primary Tool	Fallback 1	Fallback 2
PubMed_get_cited_by	EuropePMC_get_citations	OpenAlex citations
PubMed_get_related	SemanticScholar_search_papers	Keyword search
GTEx_get_median_gene_expression	HPA_get_rna_expression_by_source	Mark unavailable
InterPro_get_protein_domains	UniProt features	Mark unavailable
Unpaywall_check_oa_status	EuropePMC OA flag	OpenAlex is_oa

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Parameter Quick Reference

Literature Search

# PubMed
{'query': '"GENE"[Title]', 'limit': 100}

# OpenAlex
{'search_keywords': 'term', 'max_results': 100, 'year_from': 2020}

# With collision filter
{'query': '"TRAG" AND immune NOT plasmid NOT conjugation', 'limit': 50}

Citation Tools

{'pmid': '12345678', 'limit': 100}  # PubMed citations
{'article_id': 'MED:12345678', 'source': 'MED'}  # EuropePMC

Annotation Tools

# UniProt
{'accession': 'P38606'}
{'ids': ['P38606'], 'from_db': 'UniProtKB_AC-ID', 'to_db': 'Ensembl'}

# GTEx
{'gencode_id': 'ENSG00000114573', 'tissue': 'all'}

# InterPro
{'uniprot_accession': 'P38606'}

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Complete Alphabetical Tool List

Literature (18)

1. ArXiv_search_papers
2. BioRxiv_get_preprint (DOI retrieval)
3. Crossref_search_works
4. DBLP_search_publications
5. DOAJ_search_articles
6. EuropePMC_search_articles
7. Fatcat_search_scholar
8. HAL_search_archive
9. MedRxiv_get_preprint (DOI retrieval)
10. OpenAIRE_search_publications
11. OSF_search_preprints
12. PMC_search_papers
13. PubMed_search_articles
14. SemanticScholar_search_papers
15. Zenodo_search_records
16. openalex_literature_search
17. openalex_search_works
18. PubTator_search_entities

Citation (7)

19. EuropePMC_get_citations
20. EuropePMC_get_references
21. PubMed_get_article
22. PubMed_get_cited_by
23. PubMed_get_links
24. PubMed_get_related
25. Unpaywall_check_oa_status

Protein/Gene (15)

26. InterPro_get_protein_domains
27. MyGene_get_gene_annotation
28. UniProt_get_alternative_names_by_accession
29. UniProt_get_disease_variants_by_accession
30. UniProt_get_entry_by_accession
31. UniProt_get_function_by_accession
32. UniProt_get_ptm_processing_by_accession
33. UniProt_get_recommended_name_by_accession
34. UniProt_get_sequence_by_accession
35. UniProt_get_subcellular_location_by_accession
36. UniProt_id_mapping
37. UniProt_search
38. alphafold_get_prediction
39. ensembl_lookup_gene
40. proteins_api_get_protein

Expression (6)

41. CELLxGENE_get_expression_data
42. GTEx_get_gene_expression
43. GTEx_get_median_gene_expression
44. HPA_get_comprehensive_gene_details_by_ensembl_id
45. HPA_get_rna_expression_by_source
46. HPA_get_subcellular_location

Pathway/Function (8)

47. GO_get_annotations_for_gene
48. Reactome_map_uniprot_to_pathways
49. WikiPathways_search
50. kegg_get_gene_info
51. OpenTargets_get_target_gene_ontology_by_ensemblID
52. OpenTargets_get_target_tractability_by_ensemblID
53. OpenTargets_get_associated_drugs_by_target_ensemblID
54. OpenTargets_get_publications_by_target_ensemblID

Interaction (4)

55. STRING_get_protein_interactions
56. intact_get_interactions
57. intact_get_complex_details
58. OpenTargets_get_target_interactions_by_ensemblID

Variant/Disease (8)

59. clinvar_search_variants
60. gnomad_get_gene
61. gnomad_get_gene_constraints
62. OpenTargets_get_diseases_phenotypes_by_target_ensembl
63. OpenTargets_get_target_safety_profile_by_ensemblID
64. DGIdb_get_drug_gene_interactions
65. DGIdb_get_gene_druggability
66. HPA_get_cancer_prognostics_by_gene

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Total Tools: 66

• Literature: 18
• Citation: 7
• Protein/Gene Annotation: 15
• Expression: 6
• Pathway/Function: 8
• Interaction: 4
• Variant/Disease: 8

Last Updated: 2026-02-04 (v5.0 - Added annotation tools)