Clarivate Searches (Motif) API

The Searches (Motif) API from Clarivate — 1 operation(s) for searches (motif).

Documentation GitHub OpenAPI

Operations 1

Each operation below carries the questions people ask an LLM about it and the instructions they give an agent to run it. Generated by API Evangelist overlay

POST /reports/{report_id}/searches/motifp Run a protein motif search · Create Motif Protein search #

Ask an LLM

“How do I search for a protein motif pattern in Derwent sequences?”

“Can I add a motif search to my project?”

Tell an agent

Create a protein motif search in project {report_id}.

Start a motif protein search under project {report_id}.

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OpenAPI Specification

openapi: 3.2.0
info:
  title: Derwent Sequence Search Searches (Motif) API
  version: V1@2026-06-09
  description: OpenAPI Docs & Interactive UI
  license:
    name: Commercially Licensed Product
    url: https://clarivate.com/derwent/solutions/derwent-sequence-base/
servers:
- url: https://api.clarivate.com/derwent-sequence-search
security:
- key: []
tags:
- name: Searches (Motif)
paths:
  /reports/{report_id}/searches/motifp:
    parameters:
    - name: report_id
      in: path
      description: Report ID
      required: true
      schema:
        type: integer
    post:
      summary: Create Motif Protein search
      tags:
      - Searches (Motif)
      parameters: []
      responses:
        '201':
          description: Created
          content:
            application/json:
              examples:
                created:
                  value:
                    data:
                    - id: '47'
                      type: search
                      attributes:
                        id: 47
                        program: motifp
                        title: Motif Protein search
                        status: queued
                        completion: 0
                        search_results_count: 0
                        redundant_search_results_count: 0
                        created_at: '2026-06-09T06:50:50Z'
                        started_at: null
                        completed_at: null
                  summary: Successful motifp search creation
              schema:
                type: object
                properties:
                  data:
                    type: array
                    items:
                      $ref: '#/components/schemas/Search'
                required:
                - data
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SearchCreateParams'
            examples:
              motifp_search:
                summary: Motifp Search
                value:
                  search:
                    title: Motif Protein search
                    query: E[ED]E
                    databases:
                    - geneseq
                    - wogene
                    program_options:
                      max_target_seqs: 1000
                      max_mismatches: 2
        required: true
      operationId: postReportsByReportIdSearchesMotifp
      x-operation-id-source: derived
components:
  schemas:
    Search:
      type: object
      properties:
        id:
          type: string
          description: Unique identifier of the Search.
          example: '1'
        type:
          type: string
          description: Resource type.
          enum:
          - search
        attributes:
          $ref: '#/components/schemas/SearchAttributes'
      required:
      - id
      - type
      - attributes
    SearchCreateParams:
      oneOf:
      - $ref: '#/components/schemas/SearchCreateSingleQueryParams'
      - $ref: '#/components/schemas/SearchCreateMultiSequenceParams'
      discriminator:
        propertyName: mss
    SearchCreateMultiSequenceParams:
      type: object
      required:
      - search
      properties:
        search:
          type: object
          required:
          - program
          - queries
          - mss
          properties:
            title:
              type: string
              maxLength: 255
              description: Search title
            program:
              type: string
              enum:
              - blastn
              - blastp
              - blastx
              - tblastn
              - tblastx
              - swn
              - swp
              - cdrn
              - cdrp
              - motifn
              - motifp
              - bestseqn
              - bestseqp
              - keyword
              - modification
              - modificationn
              - modificationp
              example: blastn
              description: Search algorithm
            databases:
              type: array
              items:
                type: string
                enum:
                - usgene_patents
                - usgene_applications
                - geneseq
                - fastalert
                - wogene
                - genbank
                - genbank_pat
              description: Convenience shorthand for enabling specific databases (maps to search_options)
            exclude_geneseq_from:
              type: array
              items:
                type: string
                enum:
                - usgene
                - wogene
              description: Exclude GeneSeq documents from specified databases
            search_options:
              type: object
              description: Search-level options (thresholds, database toggles, date filters, etc.)
              properties:
                query_coverage_threshold:
                  type: number
                  description: Minimum query coverage (%)
                identities_percent_threshold:
                  type: number
                  description: Minimum identity (%)
                auto_params_for_short_sequences:
                  type: boolean
                  description: Auto-tune parameters for short sequences (blastn/blastp)
                search_usgene_patents:
                  type: boolean
                search_usgene_applications:
                  type: boolean
                search_geneseq:
                  type: boolean
                search_fastalert:
                  type: boolean
                search_wipo:
                  type: boolean
                search_genbank:
                  type: boolean
                search_genbank_pat:
                  type: boolean
                exclude_geneseq_documents_from_usgene:
                  type: boolean
                exclude_geneseq_documents_from_wipo:
                  type: boolean
                exclude_mega_patents:
                  type: boolean
                exclude_non_published_applications:
                  type: boolean
                patent_priority_date_from:
                  type: string
                  description: Filter by patent priority date (start)
                patent_priority_date_to:
                  type: string
                  description: Filter by patent priority date (end)
                patent_application_date_from:
                  type: string
                  description: Filter by patent application date (start)
                patent_application_date_to:
                  type: string
                  description: Filter by patent application date (end)
                patent_publication_date_from:
                  type: string
                  description: Filter by patent publication date (start)
                patent_publication_date_to:
                  type: string
                  description: Filter by patent publication date (end)
                cdr_mismatches:
                  type: array
                  items:
                    type: integer
                  description: Mismatch counts allowed per CDR region (heavy/light chains)
                heavy_chain_identity:
                  type: number
                  description: Heavy chain identity threshold (%)
                light_chain_identity:
                  type: number
                  description: Light chain identity threshold (%)
                individual_identities:
                  type: boolean
                  description: Whether to evaluate individual identities (MSS)
                individual_coverage:
                  type: boolean
                  description: Whether to evaluate individual query coverages (MSS)
            program_options:
              type: object
              description: Program-specific options (varies by program). Common options include evalue, gapopen, gapextend, max_target_seqs, word_size, strand, matrix, etc.
              properties:
                evalue:
                  type: number
                  description: Expectation value threshold (BLAST programs)
                gapopen:
                  type: integer
                  description: Gap opening penalty (BLAST programs)
                gapextend:
                  type: integer
                  description: Gap extension penalty (BLAST programs)
                max_target_seqs:
                  type: integer
                  minimum: 1
                  description: Max target sequences (BLAST programs)
                word_size:
                  type: integer
                  description: Word size for initial match
                strand:
                  type: string
                  enum:
                  - both
                  - minus
                  - plus
                  description: Query strand (nucleotide programs)
                matrix:
                  type: string
                  description: 'Scoring matrix (protein programs: PAM30, PAM70, BLOSUM45, BLOSUM62, BLOSUM80)'
                task:
                  type: string
                  description: BLAST sub-task (e.g. blastn, megablast)
                subject_length_min:
                  type: integer
                  minimum: 1
                  maximum: 100000
                  description: Minimum subject length
                subject_length_max:
                  type: integer
                  minimum: 1
                  maximum: 100000
                  description: Maximum subject length
                ungapped:
                  type: boolean
                  description: Perform ungapped alignment (BLAST programs)
                mat:
                  type: string
                  description: 'Scoring matrix (SW programs: DNA, NUC.4.4)'
                gapo:
                  type: integer
                  description: Gap opening penalty (SW programs)
                gape:
                  type: integer
                  description: Gap extension penalty (SW programs)
                min_score:
                  type: integer
                  minimum: 1
                  description: Minimum alignment score (SW programs)
                topscore_num:
                  type: integer
                  minimum: 1
                  description: Number of top scoring sequences (SW programs)
                reverse:
                  type: boolean
                  description: Search reverse complement (SW nucleotide)
                sequences_type:
                  type: string
                  enum:
                  - protein
                  - nucleotide
                  description: Sequences type for keyword/FTS search
                max_documents_per_source:
                  type: integer
                  description: FTS limit on documents per database source
            query_builder:
              type: object
              description: Advanced query builder filters for refining search scope
            seqmod_query_builder:
              type: object
              description: Sequence modification query builder configuration (type, position, name)
            monitor_options:
              type: object
              description: Search monitoring configuration for recurring searches
            queries:
              type: array
              items:
                type: string
              minItems: 1
              description: Multiple sequence queries in FASTA format
            mss:
              type: boolean
              enum:
              - true
              description: Must be true for multi-sequence search mode
    SearchAttributes:
      type: object
      required:
      - id
      - program
      - title
      - status
      - completion
      - search_results_count
      - redundant_search_results_count
      - created_at
      properties:
        id:
          type: integer
        program:
          type: string
        title:
          type: string
        status:
          type: string
        completion:
          type: integer
        search_results_count:
          type: integer
        redundant_search_results_count:
          type: integer
        created_at:
          type: string
          format: date-time
        started_at:
          oneOf:
          - type: string
            format: date-time
          - type: 'null'
        completed_at:
          oneOf:
          - type: string
            format: date-time
          - type: 'null'
    SearchCreateSingleQueryParams:
      type: object
      required:
      - search
      properties:
        search:
          type: object
          required:
          - program
          - query
          properties:
            title:
              type: string
              maxLength: 255
              description: Search title
            program:
              type: string
              enum:
              - blastn
              - blastp
              - blastx
              - tblastn
              - tblastx
              - swn
              - swp
              - cdrn
              - cdrp
              - motifn
              - motifp
              - bestseqn
              - bestseqp
              - keyword
              - modification
              - modificationn
              - modificationp
              example: blastn
              description: Search algorithm
            databases:
              type: array
              items:
                type: string
                enum:
                - usgene_patents
                - usgene_applications
                - geneseq
                - fastalert
                - wogene
                - genbank
                - genbank_pat
              description: Convenience shorthand for enabling specific databases (maps to search_options)
            exclude_geneseq_from:
              type: array
              items:
                type: string
                enum:
                - usgene
                - wogene
              description: Exclude GeneSeq documents from specified databases
            search_options:
              type: object
              description: Search-level options (thresholds, database toggles, date filters, etc.)
              properties:
                query_coverage_threshold:
                  type: number
                  description: Minimum query coverage (%)
                identities_percent_threshold:
                  type: number
                  description: Minimum identity (%)
                auto_params_for_short_sequences:
                  type: boolean
                  description: Auto-tune parameters for short sequences (blastn/blastp)
                search_usgene_patents:
                  type: boolean
                search_usgene_applications:
                  type: boolean
                search_geneseq:
                  type: boolean
                search_fastalert:
                  type: boolean
                search_wipo:
                  type: boolean
                search_genbank:
                  type: boolean
                search_genbank_pat:
                  type: boolean
                exclude_geneseq_documents_from_usgene:
                  type: boolean
                exclude_geneseq_documents_from_wipo:
                  type: boolean
                exclude_mega_patents:
                  type: boolean
                exclude_non_published_applications:
                  type: boolean
                patent_priority_date_from:
                  type: string
                  description: Filter by patent priority date (start)
                patent_priority_date_to:
                  type: string
                  description: Filter by patent priority date (end)
                patent_application_date_from:
                  type: string
                  description: Filter by patent application date (start)
                patent_application_date_to:
                  type: string
                  description: Filter by patent application date (end)
                patent_publication_date_from:
                  type: string
                  description: Filter by patent publication date (start)
                patent_publication_date_to:
                  type: string
                  description: Filter by patent publication date (end)
                cdr_mismatches:
                  type: array
                  items:
                    type: integer
                  description: Mismatch counts allowed per CDR region (heavy/light chains)
                heavy_chain_identity:
                  type: number
                  description: Heavy chain identity threshold (%)
                light_chain_identity:
                  type: number
                  description: Light chain identity threshold (%)
                individual_identities:
                  type: boolean
                  description: Whether to evaluate individual identities (MSS)
                individual_coverage:
                  type: boolean
                  description: Whether to evaluate individual query coverages (MSS)
            program_options:
              type: object
              description: Program-specific options (varies by program). Common options include evalue, gapopen, gapextend, max_target_seqs, word_size, strand, matrix, etc.
              properties:
                evalue:
                  type: number
                  description: Expectation value threshold (BLAST programs)
                gapopen:
                  type: integer
                  description: Gap opening penalty (BLAST programs)
                gapextend:
                  type: integer
                  description: Gap extension penalty (BLAST programs)
                max_target_seqs:
                  type: integer
                  minimum: 1
                  description: Max target sequences (BLAST programs)
                word_size:
                  type: integer
                  description: Word size for initial match
                strand:
                  type: string
                  enum:
                  - both
                  - minus
                  - plus
                  description: Query strand (nucleotide programs)
                matrix:
                  type: string
                  description: 'Scoring matrix (protein programs: PAM30, PAM70, BLOSUM45, BLOSUM62, BLOSUM80)'
                task:
                  type: string
                  description: BLAST sub-task (e.g. blastn, megablast)
                subject_length_min:
                  type: integer
                  minimum: 1
                  maximum: 100000
                  description: Minimum subject length
                subject_length_max:
                  type: integer
                  minimum: 1
                  maximum: 100000
                  description: Maximum subject length
                ungapped:
                  type: boolean
                  description: Perform ungapped alignment (BLAST programs)
                mat:
                  type: string
                  description: 'Scoring matrix (SW programs: DNA, NUC.4.4)'
                gapo:
                  type: integer
                  description: Gap opening penalty (SW programs)
                gape:
                  type: integer
                  description: Gap extension penalty (SW programs)
                min_score:
                  type: integer
                  minimum: 1
                  description: Minimum alignment score (SW programs)
                topscore_num:
                  type: integer
                  minimum: 1
                  description: Number of top scoring sequences (SW programs)
                reverse:
                  type: boolean
                  description: Search reverse complement (SW nucleotide)
                sequences_type:
                  type: string
                  enum:
                  - protein
                  - nucleotide
                  description: Sequences type for keyword/FTS search
                max_documents_per_source:
                  type: integer
                  description: FTS limit on documents per database source
            query_builder:
              type: object
              description: Advanced query builder filters for refining search scope
            seqmod_query_builder:
              type: object
              description: Sequence modification query builder configuration (type, position, name)
            monitor_options:
              type: object
              description: Search monitoring configuration for recurring searches
            query:
              type: string
              example: CGCGGTCGGGTCGTG
              description: Single sequence query string
  securitySchemes:
    key:
      type: apiKey
      in: header
      name: X-ApiKey
x-provenance:
  method: harvested
  publisher: Clarivate
  source: https://developer.clarivate.com/apis/dss-search-api/swagger
  note: split by refine-openapis from the provider's own published document, verified by fetch (openapi/_original/*.fetch.json);
    stamped by stamp-openapi-provenance.py (roadmap#793)

Clarivate Searches (Motif) API

Operations 1

Documentation

Specifications

Schemas & Data

Other Resources