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Biology Modality

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8 toolsv1.0.0
Overview

About

Biology modality intelligence platform covering biological sequence analysis, protein and nucleotide search, post-translational modification profiling, antibody-antigen interaction discovery, and multi-omics biological entity retrieval.

Capabilities

ls_sequence_search_submit

Use this tool when the user wants to launch a bio sequence search job. Tool flow: 1. Submit job to get job_id. 2. Poll status with ls_sequence_search_check_status. 3. Fetch results with ls_sequence_search_get_results after success.

Arguments
qcov_hsp_percobject

object, optional query coverage filter, format {"start": int, "end": int}

perc_identityobject

object, optional identity filter, format {"start": int, "end": int}

scov_hsp_percobject

object, optional subject coverage filter, format {"start": int, "end": int}

evaluenumber

float, expect threshold

query_type* Requiredstring

str, target sequence type, supports "NUCLEOTIDE" and "PROTEIN"

sequence* Requiredstring

str, single query sequence string

sequence_type* Requiredstring

str, query sequence type, supports "NUCLEOTIDE" and "PROTEIN"

databasearray

List[str], target database list, supports "ALLPATENT" and "CLAIMS"

strandarray

List[str], optional alignment direction filter for nucleotide searches only. Supports "PLUS" and "MINUS"; may be omitted or multi-selected.

subject_lengthobject

object, optional subject length filter, format {"start": int, "end": int}

q_perc_identityobject

object, optional query identity filter, format {"start": int, "end": int}

with_gapsboolean

bool, whether sequence alignment includes gaps

s_perc_identityobject

object, optional subject identity filter, format {"start": int, "end": int}

limitinteger

int, maximum returned result count for the backend task

has_modificationarray

List[bool], optional filter for whether the sequence has chemical modification information. Supports true and false; may be omitted or multi-selected.

ls_sequence_search_get_results

Use this tool after ls_sequence_search_check_status reports success for a job created by ls_sequence_search_submit or ls_modification_search_submit.

/api/ls/sequence/job/result

ls_sequence_search_check_status

Use this tool after ls_sequence_search_submit or ls_modification_search_submit to check the current backend status of a submitted job.

/api/ls/sequence/job/status

ls_sequence_fetch

Batch fetch full detail records by sequence number. Maximum 100 sequence numbers per request.

/api/ls/sequence/fetch

ls_sequence_alignment

Run sequence alignment. Use this tool when the user wants to align biological sequences directly. Supports PSA (pairwise) and MSA (multiple sequence alignment). query_sequence is required for PSA.

/api/ls/sequence/alignment

ls_patent_sequence_fetch

Batch fetch sequences associated with a patent by patent ID or patent number. Supports pagination with offset and limit (max 100). Either patent_id or pn must be provided.

/api/ls/patent/sequence/fetch

ls_modification_search_submit

Use this tool when the user wants to search bio sequence records by modification conditions and optionally narrow the result set with sequence length or a query sequence. Tool flow: 1. Submit job to get job_id. 2. Poll status with ls_sequence_search_check_status. 3. Fetch results with ls_sequence_search_get_results after success.

/api/ls/modification/job

ls_antibody_antigen_search

Use this tool when the user wants to find antibodies associated with a target antigen and optionally narrow the result set with facet filters.

/api/ls/antibody-antigen/search

What is Biology Modality MCP Server?

Biology modality intelligence platform covering biological sequence analysis, protein and nucleotide search, post-translational modification profiling, antibody-antigen interaction discovery, and multi-omics biological entity retrieval.

Capabilities

  • Use this tool when the user wants to launch a bio sequence search job. Tool flow: 1. Submit job to get job_id. 2. Poll status with ls_sequence_search_check_status. 3. Fetch results with ls_sequence_search_get_results after success.
  • Use this tool after ls_sequence_search_check_status reports success for a job created by ls_sequence_search_submit or ls_modification_search_submit.
  • Use this tool after ls_sequence_search_submit or ls_modification_search_submit to check the current backend status of a submitted job.
  • Batch fetch full detail records by sequence number. Maximum 100 sequence numbers per request.
  • Run sequence alignment. Use this tool when the user wants to align biological sequences directly. Supports PSA (pairwise) and MSA (multiple sequence alignment). query_sequence is required for PSA.
  • Batch fetch sequences associated with a patent by patent ID or patent number. Supports pagination with offset and limit (max 100). Either patent_id or pn must be provided.
  • Use this tool when the user wants to search bio sequence records by modification conditions and optionally narrow the result set with sequence length or a query sequence. Tool flow: 1. Submit job to get job_id. 2. Poll status with ls_sequence_search_check_status. 3. Fetch results with ls_sequence_search_get_results after success.
  • Use this tool when the user wants to find antibodies associated with a target antigen and optionally narrow the result set with facet filters.

How to connect

Get a Patsnap Open Platform API key, copy the MCP connection URL from the Connect panel on this page, and add the server to Cursor, Claude Desktop, or another Model Context Protocol-compatible AI agent client.

Example MCP configuration

{
  "mcpServers": {
    "biology_modality": {
      "url": "https://connect.patsnap.com/06e741/logic-mcp?apikey={your_api_key}"
    }
  }
}

Use cases

  • Use Biology Modality MCP Server to let AI agents access Patsnap innovation intelligence inside agent conversations.

FAQ

What is Biology Modality MCP Server?
Biology Modality MCP Server is a Patsnap Open Platform Model Context Protocol server that exposes innovation intelligence tools for AI agents and LLM clients.
How does Biology Modality MCP Server work with AI agents?
An MCP-compatible client connects to the server URL with your Patsnap Open Platform API key, discovers available tools, and lets the model call Patsnap data and capabilities during conversations.
What tasks can Biology Modality MCP Server perform?
Biology Modality MCP Server exposes Patsnap tools through the Model Context Protocol so AI agents can retrieve patents, papers, and innovation intelligence during multi-step reasoning.
How do I connect this MCP server to an agent?
Get a Patsnap Open Platform API key, copy the MCP connection URL or JSON config from this page, and add it to your MCP-compatible client following the MCP Quick Start guide.