mirror of
https://github.com/mims-harvard/ToolUniverse.git
synced 2026-09-19 07:31:47 +08:00
Shanghua Gao
08246bcd4d
* docs: expand redirect map with 15 additional legacy paths Adds redirects for paths uncovered in a second-pass audit against the live published site. Each destination verified to return HTTP 200 on https://zitniklab.hms.harvard.edu/ToolUniverse/. New /tutorials/ → /guide/, /tools/, /expand_tooluniverse/ redirects: - make_your_data_searchable, make_your_data_agent_searchable, build_search_and_share_datastores → guide/make_your_data_agent_searchable - skills → guide/skills_showcase - tool_finder → guide/finding_tools - overview → guide/index - remote_tools → tools/remote_tools - mcp_integration → expand_tooluniverse/remote_tools/mcp_integration Top-level legacy pages (404 at root, now redirected): - getting_started → guide/python_guide - deployment, contributing, changelog → about/<page> - faq → help/faq Local build confirms all 22 redirect stubs generate and that every destination file exists in the build output. * docs: fix broken sphinx-tabs, dead toctrees, orphan pages, missing image Build now produces 0 warnings/errors of these structural categories (down from ~280 such issues): - Re-enable sphinx_tabs.tabs extension (3.5.0 supports Sphinx 9.x); fixes 7 broken "Unknown directive type tabs" errors that made help/faq.html and help/troubleshooting.html render incomplete. - Drop 25+ dead toctree entries in api/modules.rst and api/tooluniverse.rst that referenced per-module pages never generated by sphinx-apidoc; modules.rst now points at the existing comprehensive tooluniverse autodoc page. - Wire 16 orphan pages into the master toctree so they're reachable from the navigation, including tooluniverse_case_study, visualization_tutorial, expert_feedback, literature_search_web_ui, euhealth, logging, openrouter, streaming, vllm, wechat_community, simbad_tools, the guide/index landing page, and the full expand_tooluniverse sub-tree. - Remove three stale ":doc:" links to old/{quickstart,installation, getting_started} from sitemap.rst (those directories are excluded from the build) and mark sitemap.rst as :orphan: since it's a parallel nav surface by design. - Mark MCP_TASKS_GUIDE.md as orphan and exclude the internal DOCUMENTATION_STRUCTURE.md meta-doc from the build. - Add the missing tools/remote/ui.jpg referenced by the remote expert_feedback page (previously: broken image). * docs: eliminate all 49 structural Sphinx ERRORs (broken tables, directives, headings) Round-3 build cleanup. Builds now finish with 0 structural ERRORs of any category (previous: 49 ERRORs spread across 20 files). Total warnings/errors dropped from 280 → 114; the remaining 114 are all in Python source-file docstrings (out of scope for a docs PR). Categories fixed: **Malformed tables** (8 files) Replace ASCII grid tables with mis-aligned pipes and inline-markdown pipe tables (which RST mis-parses as substitution references) with ``list-table`` directives that render correctly across all themes: - guide/literature_search_tools_tutorial.rst (two tables) - guide/cache_system.rst (env-var table whose first column overflowed) - guide/clinical_guidelines_tools.rst - guide/make_your_data_agent_searchable.rst - expand_tooluniverse/contributing/index.rst - expand_tooluniverse/contributing/remote_tools.rst - expand_tooluniverse/reference/index.rst **list-table indentation** (3 files) Option lines and list items were indented with 1 space (only valid for 3-space) so Sphinx silently dropped them and reported "exactly one bullet list expected": - guide/finding_tools.rst - guide/http_api.rst - guide/tools.rst **Code-block separators** (5 files, ~30 directives) Add the required blank line between an introductory paragraph and a following ``.. code-block::``. Without it, Sphinx treated the directive as a continuation of the paragraph and emitted "Unexpected indentation" for every line of the code: - guide/literature_search_tools_tutorial.rst - expand_tooluniverse/quick_start.rst - expand_tooluniverse/contributing/local_tools.rst - expand_tooluniverse/contributing/remote_tools.rst - guide/make_your_data_agent_searchable.rst **Heading-style + indentation** (3 files) - guide/building_ai_scientists/mcp_name_shortening.rst — strip stray leading spaces from two section titles + downgrade unknown ``.. critical::`` to ``.. important::`` - about/deployment.rst — remove rogue ``=========`` underline below numbered-list items that mis-led the parser into skipping heading levels - guide/make_your_data_agent_searchable.rst — extend four "title underline too short" underlines + convert four markdown ``` fences to RST literal blocks **Misc directive / target fixes** - guide/python_guide.rst — replace nonexistent ``.. success::`` with a tip-styled ``.. admonition::`` - guide/euhealth_tools_tutorial.rst — indent ``.. note::`` body so it is no longer an empty admonition - help/troubleshooting.rst — same fix + remove rogue ``=========`` line that was being read as a section overline - tools/cellosaurus_tools.rst — wrap ``CVCL_`` in literal backticks so the trailing underscore stops triggering missing-target lookups - expand_tooluniverse/index.rst — promote two leading-space bullet lists to standalone lists so the indentation is correct - expand_tooluniverse/reference/architecture.rst — switch ``.. graphviz::`` (extension not installed) to a plain ``.. code-block:: text``; the embedded content was Mermaid pseudo-code anyway - guide/tools.rst — strip leading space on a section title * docs: clear all remaining content warnings (lists, headings, refs, grids) Round-4 build cleanup. Builds now finish with 0 structural ERRORs and 0 content WARNINGs; the only remaining ~11 warnings are pre-existing autodoc infrastructure noise (duplicate object index entries from autosummary, and the ghost_tool / medrxiv_tool modules that genuinely fail to import) — none are in hand-written documentation. Fixes in this commit: **sphinx-design grids** (python_guide.rst) Re-indent two ``.. grid::`` blocks whose first card + options used 1-space indentation (Sphinx silently dropped them → "parent of grid-item should be grid-row"). Also fix a ``.. button-ref::`` whose content was indented 1 space, producing a broken ``:any:`` cross-reference, and point it at the absolute ``/api/modules``. **Numbered/bulleted sub-lists** (tool_composition, literature_search ×2, architecture, literature_search_web_ui, make_your_data, agentic_tools, finding_tools, euhealth) Insert the required blank line before nested lists and re-indent 1-space sub-bullets to align under their parent list marker. Clears ~80 "list ends without a blank line; unexpected unindent" warnings. **Title underlines** (logging, tool_caller, loading_tools, tool_composition, euhealth, make_your_data, contributing/local_tools, reference/index, remote_tools/tutorial, troubleshooting + bulk pass) Extend underlines shorter than their title text; strip stray leading spaces from section titles that Sphinx read as block quotes. **Stray markdown in RST** (make_your_data, local_tools) Convert leftover ``###`` headings and ``` ``` fences to proper RST directives; remove a rogue ``------`` separator that was being parsed as a section underline. **Duplicate autosectionlabel** (make_your_data) Rename the second "How it works" heading to "How sharing works". **uniprot_tools** (JSON + generated RST) Rephrase the ``min_length`` / ``max_length`` descriptions so the open-ended range syntax no longer contains a bare ``*`` that RST read as an unterminated emphasis marker. Fixed in the JSON source so it survives doc regeneration.
2594 lines
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ReStructuredText
2594 lines
83 KiB
ReStructuredText
Available Tools
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==========================
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ToolUniverse provides over 1000 scientific tools organized into local and remote categories. This overview helps you discover and navigate the available tools for your research needs.
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Tool Registry
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---------------
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Local Tools
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~~~~~~~~~~~
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Local tools are Python classes that run within the ToolUniverse process, providing high performance and seamless integration.
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**Key Features:**
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- High performance with no network overhead
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- Automatic discovery and registration
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- Full access to ToolUniverse features
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- Easy development and testing
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Remote Tools
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~~~~~~~~~~~~
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Remote tools integrate external services, APIs, and specialized systems running on different servers.
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**Key Features:**
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- Integration with external APIs and services
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- Scalable computation offloading
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- Support for different programming languages
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- Secure isolation of sensitive operations
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.. tip::
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**Discover Available Tools:**
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* :doc:`../guide/listing_tools` - Browse tools by category and explore the full catalog
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* :doc:`../guide/finding_tools` - Learn advanced search techniques and filters
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* :doc:`../tools/remote_tools` - Set up remote tool integrations
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* :doc:`../guide/loading_tools` - Load and configure local tools
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Overview
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-----------------------------
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* **Total Configuration Files**: 141
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* **Total Tools**: 834
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Local Tools
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-----------
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.. note::
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Tools running within the ToolUniverse process
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Packages Tools
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. toctree::
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:maxdepth: 1
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Bioinformatics Core Tools <bioinformatics_core_tools>
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.. toctree::
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:maxdepth: 1
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Cheminformatics Tools <cheminformatics_tools>
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.. toctree::
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:maxdepth: 1
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Earth Sciences Tools <earth_sciences_tools>
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.. toctree::
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:maxdepth: 1
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Genomics Tools <genomics_tools>
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:maxdepth: 1
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Image Processing Tools <image_processing_tools>
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.. toctree::
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:maxdepth: 1
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Machine Learning Tools <machine_learning_tools>
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.. toctree::
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:maxdepth: 1
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Neuroscience Tools <neuroscience_tools>
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.. toctree::
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:maxdepth: 1
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Physics Astronomy Tools <physics_astronomy_tools>
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.. toctree::
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:maxdepth: 1
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SIMBAD Astronomy Tools <simbad_tools>
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:maxdepth: 1
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Scientific Computing Tools <scientific_computing_tools>
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:maxdepth: 1
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Single Cell Tools <single_cell_tools>
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.. toctree::
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:maxdepth: 1
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Structural Biology Tools <structural_biology_tools>
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:maxdepth: 1
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Visualization Tools <visualization_tools>
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Builtin Tools
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Admetai Tools <admetai_tools>
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Adverse Event Tools <adverse_event_tools>
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Agentic Tools <agentic_tools>
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Alphafold Tools <alphafold_tools>
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Arxiv Tools <arxiv_tools>
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Biomodels Tools <biomodels_tools>
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:maxdepth: 1
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Biorxiv Tools <biorxiv_tools>
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:maxdepth: 1
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Blast Tools <blast_tools>
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.. toctree::
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:maxdepth: 1
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Boltz Mcp Loader Tools <boltz_mcp_loader_tools>
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.. toctree::
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:maxdepth: 1
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Cbioportal Tools <cbioportal_tools>
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.. toctree::
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:maxdepth: 1
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Cdc Tools <cdc_tools>
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.. toctree::
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Cellosaurus Tools <cellosaurus_tools>
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.. toctree::
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Chembl Tools <chembl_tools>
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Clinical Trials Tools <clinical_trials_tools>
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.. toctree::
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:maxdepth: 1
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Clinicaltrials Gov Tools <clinicaltrials_gov_tools>
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Clinvar Tools <clinvar_tools>
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Compact Mode Tools <compact_mode_tools>
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Compose Tools <compose_tools>
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Core Tools <core_tools>
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Crossref Tools <crossref_tools>
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Dailymed Tools <dailymed_tools>
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Dataset Tools <dataset_tools>
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Dblp Tools <dblp_tools>
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Dbpedia Tools <dbpedia_tools>
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Dbsnp Tools <dbsnp_tools>
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Disease Target Score Tools <disease_target_score_tools>
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.. toctree::
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Doaj Tools <doaj_tools>
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Drug Discovery Agents <drug_discovery_agents>
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.. toctree::
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Efo Tools <efo_tools>
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Embedding Tools <embedding_tools>
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Emdb Tools <emdb_tools>
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Encode Tools <encode_tools>
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Enrichr Tools <enrichr_tools>
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Ensembl Tools <ensembl_tools>
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Euhealth Tools <euhealth_tools>
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Europe Pmc Tools <europe_pmc_tools>
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.. toctree::
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Expert Feedback Tools <expert_feedback_tools>
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.. toctree::
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Fatcat Tools <fatcat_tools>
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.. toctree::
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Fda Drug Adverse Event Detail Tools <fda_drug_adverse_event_detail_tools>
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.. toctree::
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:maxdepth: 1
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Fda Drug Adverse Event Tools <fda_drug_adverse_event_tools>
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.. toctree::
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Fda Drug Labeling Tools <fda_drug_labeling_tools>
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.. toctree::
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File Download Tools <file_download_tools>
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.. toctree::
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Finder Tools <finder_tools>
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.. toctree::
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Gbif Tools <gbif_tools>
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.. toctree::
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Gdc Tools <gdc_tools>
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.. toctree::
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Gene Ontology Tools <gene_ontology_tools>
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.. toctree::
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Geo Tools <geo_tools>
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Gnomad Tools <gnomad_tools>
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.. toctree::
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Gtex Tools <gtex_tools>
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.. toctree::
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Gtopdb Tools <gtopdb_tools>
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.. toctree::
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Gwas Tools <gwas_tools>
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.. toctree::
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Hal Tools <hal_tools>
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.. toctree::
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Hca Tools <hca_tools>
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.. toctree::
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Health Disparities Tools <health_disparities_tools>
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.. toctree::
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Hpa Tools <hpa_tools>
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.. toctree::
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Humanbase Tools <humanbase_tools>
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.. toctree::
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Idmap Tools <idmap_tools>
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Iedb Tools <iedb_tools>
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.. toctree::
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Interpro Tools <interpro_tools>
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Jaspar Tools <jaspar_tools>
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Kegg Tools <kegg_tools>
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Literature Search Tools <literature_search_tools>
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.. toctree::
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Markitdown Tools <markitdown_tools>
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.. toctree::
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Mcp Client Tools Example <mcp_client_tools_example>
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.. toctree::
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Medlineplus Tools <medlineplus_tools>
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Medrxiv Tools <medrxiv_tools>
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Mgnify Tools <mgnify_tools>
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Molecule 2D Tools <molecule_2d_tools>
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Molecule 3D Tools <molecule_3d_tools>
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Monarch Tools <monarch_tools>
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Mpd Tools <mpd_tools>
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Nhanes Tools <nhanes_tools>
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Obis Tools <obis_tools>
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Odphp Tools <odphp_tools>
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Ols Tools <ols_tools>
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Openaire Tools <openaire_tools>
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Openalex Tools <openalex_tools>
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.. toctree::
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Opentarget Tools <opentarget_tools>
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.. toctree::
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Optimizer Tools <optimizer_tools>
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.. toctree::
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Osf Preprints Tools <osf_preprints_tools>
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.. toctree::
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Output Summarization Tools <output_summarization_tools>
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.. toctree::
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Package Discovery Tools <package_discovery_tools>
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.. toctree::
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Paleobiology Tools <paleobiology_tools>
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.. toctree::
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:maxdepth: 1
|
|
|
|
Pathway Commons Tools <pathway_commons_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pmc Tools <pmc_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Ppi Tools <ppi_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pride Tools <pride_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Protein Structure 3D Tools <protein_structure_3d_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pubchem Tools <pubchem_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pubmed Tools <pubmed_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pubtator Tools <pubtator_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Pypi Package Inspector Tools <pypi_package_inspector_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Python Executor Tools <python_executor_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Rcsb Pdb Tools <rcsb_pdb_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Rcsb Search Tools <rcsb_search_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Reactome Tools <reactome_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Regulomedb Tools <regulomedb_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Remap Tools <remap_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Rnacentral Tools <rnacentral_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Rxnorm Tools <rxnorm_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Screen Tools <screen_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Semantic Scholar Tools <semantic_scholar_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Smolagent Tools <smolagent_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Special Tools <special_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Tool Composition Tools <tool_composition_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Tool Discovery Agents <tool_discovery_agents>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Txagent Client Tools <txagent_client_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Umls Tools <umls_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Unified Guideline Tools <unified_guideline_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Uniprot Tools <uniprot_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Unpaywall Tools <unpaywall_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Url Fetch Tools <url_fetch_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Uspto Downloader Tools <uspto_downloader_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Uspto Tools <uspto_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Web Search Tools <web_search_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Who Gho Tools <who_gho_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Wikidata Sparql Tools <wikidata_sparql_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Wikipathways Tools <wikipathways_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Wikipedia Tools <wikipedia_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Worms Tools <worms_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Xml Tools <xml_tools>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Zenodo Tools <zenodo_tools>
|
|
|
|
|
|
Remote Tools
|
|
------------
|
|
|
|
.. note::
|
|
Tools registered in with remote registry
|
|
|
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
Boltz Tools <boltz_tools>
|
|
Depmap Tools <depmap_tools>
|
|
Expert Feedback Tools <expert_feedback_tools>
|
|
Immune Compass Tools <immune_compass_tools>
|
|
Pinnacle Tools <pinnacle_tools>
|
|
Transcriptformer Tools <transcriptformer_tools>
|
|
Uspto Downloader Tools <uspto_downloader_tools>
|
|
|
|
|
|
Tools by Type
|
|
-------------
|
|
|
|
**ADMETAITool** (9 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ADMETAI_predict_BBB_penetrance (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_CYP_interactions (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_bioavailability (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_clearance_distribution (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_nuclear_receptor_activity (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_physicochemical_properties (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_solubility_lipophilicity_hydration (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_stress_response (from :doc:`admetai_tools`)
|
|
* ADMETAI_predict_toxicity (from :doc:`admetai_tools`)
|
|
|
|
**AgenticTool** (52 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ADMETAnalyzerAgent (from :doc:`drug_discovery_agents`)
|
|
* AdvancedCodeQualityAnalyzer (from :doc:`agentic_tools`)
|
|
* AdverseEventICDMapper (from :doc:`adverse_event_tools`)
|
|
* AdverseEventPredictionQuestionGenerator (from :doc:`adverse_event_tools`)
|
|
* AdverseEventPredictionQuestionGeneratorWithContext (from :doc:`adverse_event_tools`)
|
|
* ArgumentDescriptionOptimizer (from :doc:`optimizer_tools`)
|
|
* ClinicalTrialDesignAgent (from :doc:`drug_discovery_agents`)
|
|
* CodeQualityAnalyzer (from :doc:`tool_discovery_agents`)
|
|
* CompoundDiscoveryAgent (from :doc:`drug_discovery_agents`)
|
|
* DataAnalysisValidityReviewer (from :doc:`agentic_tools`)
|
|
* DescriptionAnalyzer (from :doc:`agentic_tools`)
|
|
* DescriptionAnalyzer (from :doc:`optimizer_tools`)
|
|
* DescriptionQualityEvaluator (from :doc:`agentic_tools`)
|
|
* DescriptionQualityEvaluator (from :doc:`optimizer_tools`)
|
|
* DiseaseAnalyzerAgent (from :doc:`drug_discovery_agents`)
|
|
* DomainExpertValidator (from :doc:`agentic_tools`)
|
|
* DrugInteractionAnalyzerAgent (from :doc:`drug_discovery_agents`)
|
|
* DrugOptimizationAgent (from :doc:`drug_discovery_agents`)
|
|
* EthicalComplianceReviewer (from :doc:`agentic_tools`)
|
|
* ExperimentalDesignScorer (from :doc:`agentic_tools`)
|
|
* HypothesisGenerator (from :doc:`agentic_tools`)
|
|
* IntentAnalyzerAgent (from :doc:`literature_search_tools`)
|
|
* KeywordExtractorAgent (from :doc:`literature_search_tools`)
|
|
* LabelGenerator (from :doc:`agentic_tools`)
|
|
* LiteratureContextReviewer (from :doc:`agentic_tools`)
|
|
* LiteratureSynthesisAgent (from :doc:`drug_discovery_agents`)
|
|
* MedicalLiteratureReviewer (from :doc:`agentic_tools`)
|
|
* MedicalTermNormalizer (from :doc:`agentic_tools`)
|
|
* MethodologyRigorReviewer (from :doc:`agentic_tools`)
|
|
* NoveltySignificanceReviewer (from :doc:`agentic_tools`)
|
|
* OverallSummaryAgent (from :doc:`literature_search_tools`)
|
|
* PackageAnalyzer (from :doc:`tool_discovery_agents`)
|
|
* ProtocolOptimizer (from :doc:`agentic_tools`)
|
|
* QualityCheckerAgent (from :doc:`literature_search_tools`)
|
|
* QuestionRephraser (from :doc:`agentic_tools`)
|
|
* ReferenceInfoAnalyzer (from :doc:`tool_discovery_agents`)
|
|
* ReproducibilityTransparencyReviewer (from :doc:`agentic_tools`)
|
|
* ResultSummarizerAgent (from :doc:`literature_search_tools`)
|
|
* ResultsInterpretationReviewer (from :doc:`agentic_tools`)
|
|
* ScientificTextSummarizer (from :doc:`agentic_tools`)
|
|
* TestCaseGenerator (from :doc:`optimizer_tools`)
|
|
* TestResultsAnalyzer (from :doc:`tool_discovery_agents`)
|
|
* ToolCompatibilityAnalyzer (from :doc:`tool_composition_tools`)
|
|
* ToolMetadataGenerator (from :doc:`agentic_tools`)
|
|
* ToolMetadataStandardizer (from :doc:`agentic_tools`)
|
|
* ToolOutputSummarizer (from :doc:`output_summarization_tools`)
|
|
* ToolQualityEvaluator (from :doc:`agentic_tools`)
|
|
* ToolRelationshipDetector (from :doc:`agentic_tools`)
|
|
* UnifiedToolGenerator (from :doc:`tool_discovery_agents`)
|
|
* WritingPresentationReviewer (from :doc:`agentic_tools`)
|
|
* XMLToolOptimizer (from :doc:`tool_discovery_agents`)
|
|
* call_agentic_human (from :doc:`agentic_tools`)
|
|
|
|
**AlphaFoldRESTTool** (3 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* alphafold_get_annotations (from :doc:`alphafold_tools`)
|
|
* alphafold_get_prediction (from :doc:`alphafold_tools`)
|
|
* alphafold_get_summary (from :doc:`alphafold_tools`)
|
|
|
|
**ArXivTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ArXiv_search_papers (from :doc:`arxiv_tools`)
|
|
|
|
**BinaryDownloadTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* download_binary_file (from :doc:`file_download_tools`)
|
|
|
|
**BioGRIDRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* BioGRID_get_interactions (from :doc:`ppi_tools`)
|
|
|
|
**BioModelsTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* biomodels_get_files (from :doc:`biomodels_tools`)
|
|
* biomodels_search (from :doc:`biomodels_tools`)
|
|
|
|
**BioRxivTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* BioRxiv_search_preprints (from :doc:`biorxiv_tools`)
|
|
|
|
**CBioPortalRESTTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cBioPortal_get_cancer_studies (from :doc:`cbioportal_tools`)
|
|
* cBioPortal_get_mutations (from :doc:`cbioportal_tools`)
|
|
|
|
**CDCRESTTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cdc_data_get_dataset (from :doc:`cdc_tools`)
|
|
* cdc_data_search_datasets (from :doc:`cdc_tools`)
|
|
|
|
**CMAGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* CMA_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**CellosaurusGetCellLineInfoTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cellosaurus_get_cell_line_info (from :doc:`cellosaurus_tools`)
|
|
|
|
**CellosaurusQueryConverterTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cellosaurus_query_converter (from :doc:`cellosaurus_tools`)
|
|
|
|
**CellosaurusSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cellosaurus_search_cell_lines (from :doc:`cellosaurus_tools`)
|
|
|
|
**ChEMBLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ChEMBL_search_similar_molecules (from :doc:`chembl_tools`)
|
|
|
|
**ClinVarGetClinicalSignificance** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* clinvar_get_clinical_significance (from :doc:`clinvar_tools`)
|
|
|
|
**ClinVarGetVariantDetails** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* clinvar_get_variant_details (from :doc:`clinvar_tools`)
|
|
|
|
**ClinVarSearchVariants** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* clinvar_search_variants (from :doc:`clinvar_tools`)
|
|
|
|
**ClinicalTrialsDetailsTool** (9 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* extract_clinical_trial_adverse_events (from :doc:`clinicaltrials_gov_tools`)
|
|
* extract_clinical_trial_outcomes (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_conditions_and_interventions (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_descriptions (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_eligibility_criteria (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_locations (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_outcome_measures (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_references (from :doc:`clinicaltrials_gov_tools`)
|
|
* get_clinical_trial_status_and_dates (from :doc:`clinicaltrials_gov_tools`)
|
|
|
|
**ClinicalTrialsGovTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* clinical_trials_get_details (from :doc:`clinical_trials_tools`)
|
|
* clinical_trials_search (from :doc:`clinical_trials_tools`)
|
|
|
|
**ClinicalTrialsSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* search_clinical_trials (from :doc:`clinicaltrials_gov_tools`)
|
|
|
|
**ComposeTool** (11 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* BiomarkerDiscoveryWorkflow (from :doc:`compose_tools`)
|
|
* ComprehensiveDrugDiscoveryPipeline (from :doc:`compose_tools`)
|
|
* DrugSafetyAnalyzer (from :doc:`compose_tools`)
|
|
* LiteratureSearchTool (from :doc:`compose_tools`)
|
|
* MultiAgentLiteratureSearch (from :doc:`literature_search_tools`)
|
|
* OutputSummarizationComposer (from :doc:`output_summarization_tools`)
|
|
* ToolDescriptionOptimizer (from :doc:`optimizer_tools`)
|
|
* ToolDiscover (from :doc:`tool_discovery_agents`)
|
|
* ToolGraphComposer (from :doc:`tool_composition_tools`)
|
|
* ToolGraphGenerationPipeline (from :doc:`compose_tools`)
|
|
* ToolMetadataGenerationPipeline (from :doc:`compose_tools`)
|
|
|
|
**CoreTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* CORE_search_papers (from :doc:`core_tools`)
|
|
|
|
**CrossrefTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Crossref_search_works (from :doc:`crossref_tools`)
|
|
|
|
**DBLPTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* DBLP_search_publications (from :doc:`dblp_tools`)
|
|
|
|
**DBpediaSPARQLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* DBpedia_SPARQL_query (from :doc:`dbpedia_tools`)
|
|
|
|
**DOAJTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* DOAJ_search_articles (from :doc:`doaj_tools`)
|
|
|
|
**DatasetTool** (7 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* dict_search (from :doc:`dataset_tools`)
|
|
* dili_search (from :doc:`dataset_tools`)
|
|
* diqt_search (from :doc:`dataset_tools`)
|
|
* drugbank_full_search (from :doc:`dataset_tools`)
|
|
* drugbank_links_search (from :doc:`dataset_tools`)
|
|
* drugbank_vocab_filter (from :doc:`dataset_tools`)
|
|
* drugbank_vocab_search (from :doc:`dataset_tools`)
|
|
|
|
**DiseaseTargetScoreTool** (10 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* cancer_biomarkers_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* cancer_gene_census_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* chembl_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* europepmc_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* eva_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* eva_somatic_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* expression_atlas_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* genomics_england_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
* reactome_disease_target_score (from :doc:`disease_target_score_tools`)
|
|
|
|
**DynamicPackageDiscovery** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* dynamic_package_discovery (from :doc:`package_discovery_tools`)
|
|
|
|
**EFOTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OSL_get_efo_id_by_disease_name (from :doc:`efo_tools`)
|
|
|
|
**EMDBRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* EMDB_get_structure (from :doc:`emdb_tools`)
|
|
|
|
**ENCODEFilesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ENCODE_list_files (from :doc:`encode_tools`)
|
|
|
|
**ENCODESearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ENCODE_search_experiments (from :doc:`encode_tools`)
|
|
|
|
**EmbeddingDatabase** (3 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* embedding_database_add (from :doc:`embedding_tools`)
|
|
* embedding_database_create (from :doc:`embedding_tools`)
|
|
* embedding_database_search (from :doc:`embedding_tools`)
|
|
|
|
**EmbeddingSync** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* embedding_sync_download (from :doc:`embedding_tools`)
|
|
* embedding_sync_upload (from :doc:`embedding_tools`)
|
|
|
|
**EnrichrTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* enrichr_gene_enrichment_analysis (from :doc:`enrichr_tools`)
|
|
|
|
**EnsemblGetSequence** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ensembl_get_sequence (from :doc:`ensembl_tools`)
|
|
|
|
**EnsemblGetVariants** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ensembl_get_variants (from :doc:`ensembl_tools`)
|
|
|
|
**EnsemblLookupGene** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ensembl_lookup_gene (from :doc:`ensembl_tools`)
|
|
|
|
**EuHealthDeepDiveTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* euhealthinfo_deepdive (from :doc:`euhealth_tools`)
|
|
|
|
**EuHealthTopicSearchTool** (20 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* euhealthinfo_search_alcohol_tobacco_psychoactive_use (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_births (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_cancer (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_cancer_registry (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_causes_of_death (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_covid_19 (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_deaths (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_diabetes_mellitus_epidemiology_registry (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_disability (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_healthcare_expenditure (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_hospital_in_patient_data (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_infectious_diseases (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_key_indicators_registries_surveys (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_mental_health (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_obesity (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_population_health_survey (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_primary_care_workforce (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_surveillance (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_surveillance_mortality_rates (from :doc:`euhealth_tools`)
|
|
* euhealthinfo_search_vaccination (from :doc:`euhealth_tools`)
|
|
|
|
**EuropePMCGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* EuropePMC_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**EuropePMCTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* EuropePMC_search_articles (from :doc:`europe_pmc_tools`)
|
|
|
|
**ExecuteTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* execute_tool (from :doc:`compact_mode_tools`)
|
|
|
|
**FDACountAdditiveReactionsTool** (6 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FAERS_count_additive_administration_routes (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_additive_adverse_reactions (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_additive_event_reports_by_country (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_additive_reaction_outcomes (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_additive_reports_by_reporter_country (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_additive_seriousness_classification (from :doc:`fda_drug_adverse_event_tools`)
|
|
|
|
**FDADrugAdverseEventDetailTool** (5 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FAERS_search_adverse_event_reports (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
* FAERS_search_reports_by_drug_and_indication (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
* FAERS_search_reports_by_drug_and_outcome (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
* FAERS_search_reports_by_drug_and_reaction (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
* FAERS_search_serious_reports_by_drug (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
|
|
**FDADrugAdverseEventTool** (9 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FAERS_count_country_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_death_related_by_drug (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_drug_routes_by_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_drugs_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_outcomes_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_patient_age_distribution (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_reactions_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_reportercountry_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
* FAERS_count_seriousness_by_drug_event (from :doc:`fda_drug_adverse_event_tools`)
|
|
|
|
**FDADrugInteractionDetailTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FAERS_search_reports_by_drug_combination (from :doc:`fda_drug_adverse_event_detail_tools`)
|
|
|
|
**FDADrugLabel** (155 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FDA_get_abuse_dependence_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_abuse_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_accessories_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_active_ingredient_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_adverse_reactions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_alarms_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_animal_pharmacology_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_assembly_installation_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_boxed_warning_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_brand_name_generic_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_calibration_instructions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_carcinogenic_mutagenic_fertility_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_child_safety_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_clinical_pharmacology_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_clinical_studies_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_contact_for_questions_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_contraindications_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_controlled_substance_DEA_schedule_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_dear_health_care_provider_letter_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_dependence_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_disposal_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_do_not_use_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_document_id_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_dosage_and_storage_information_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_dosage_forms_and_strengths_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_interactions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_SPL_ID (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_adverse_reaction (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_calibration_instructions (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_dependence_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_document_id (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_dosage_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_environmental_warning (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_inactive_ingredient (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_labor_and_delivery_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_microbiology (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_other_safety_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_pharmacodynamics (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_pharmacogenomics (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_precautions (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_pregnancy_or_breastfeeding_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_principal_display_panel (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_reference (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_set_id (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_stop_use_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_storage_and_handling_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_by_warnings (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_name_from_patient_package_insert (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_abuse_dependence_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_abuse_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_accessories (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_active_ingredient (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_alarm (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_animal_pharmacology_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_application_number_NDC_number (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_assembly_installation_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_boxed_warning (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_child_safety_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_clinical_pharmacology (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_clinical_studies (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_consulting_doctor_pharmacist_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_contraindications (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_controlled_substance_DEA_schedule (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_dear_health_care_provider_letter_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_disposal_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_dosage_forms_and_strengths_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_drug_interactions (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_effective_time (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_food_safety_warnings (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_general_precautions (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_geriatric_use (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_health_claim (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_indication (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_info_for_nursing_mothers (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_information_for_owners_or_caregivers (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_ingredient (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_instructions_for_use (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_lab_test_interference (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_lab_tests (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_mechanism_of_action (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_medication_guide (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_nonclinical_toxicology_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_nonteratogenic_effects (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_overdosage_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_pediatric_use (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_pharmacokinetics (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_population_use (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_pregnancy_effects_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_residue_warning (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_risk (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_route (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_safe_handling_warning (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_safety_summary (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_spl_indexing_data_elements (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_teratogenic_effects (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_user_safety_warning (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drug_names_by_warnings_and_cautions (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_drugs_by_carcinogenic_mutagenic_fertility (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_effective_time_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_environmental_warning_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_general_precautions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_geriatric_use_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_health_claims_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_inactive_ingredient_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_indications_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_info_for_nursing_mothers_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_info_for_patients_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_information_for_owners_or_caregivers_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_ingredients_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_instructions_for_use_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_lab_test_interference_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_lab_tests_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_labor_and_delivery_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_manufacturer_name_NDC_number_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_mechanism_of_action_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_medication_guide_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_microbiology_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_nonclinical_toxicology_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_nonteratogenic_effects_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_other_safety_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_overdosage_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_patient_package_insert_from_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pediatric_use_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pharmacodynamics_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pharmacogenomics_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pharmacokinetics_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_population_use_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_precautions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pregnancy_effects_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_pregnancy_or_breastfeeding_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_principal_display_panel_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_purpose_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_recent_changes_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_reference_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_residue_warning_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_risk_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_route_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_safe_handling_warnings_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_safety_summary_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_spl_indexing_data_elements_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_spl_unclassified_section_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_stop_use_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_storage_and_handling_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_teratogenic_effects_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_user_safety_warning_by_drug_names (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_warnings_and_cautions_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_warnings_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_get_when_using_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_retrieve_device_use_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_retrieve_drug_name_by_device_use (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_retrieve_drug_names_by_patient_medication_info (from :doc:`fda_drug_labeling_tools`)
|
|
* FDA_retrieve_patient_medication_info_by_drug_name (from :doc:`fda_drug_labeling_tools`)
|
|
|
|
**FDADrugLabelAggregated** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FDA_get_drug_names_by_indication_aggregated (from :doc:`fda_drug_labeling_tools`)
|
|
|
|
**FDADrugLabelGetDrugGenericNameTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FDA_get_drug_generic_name (from :doc:`fda_drug_labeling_tools`)
|
|
|
|
**FDADrugLabelStats** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* FDA_get_drug_names_by_indication_stats (from :doc:`fda_drug_labeling_tools`)
|
|
|
|
**FatcatScholarTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Fatcat_search_scholar (from :doc:`fatcat_tools`)
|
|
|
|
**FileDownloadTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* download_file (from :doc:`file_download_tools`)
|
|
|
|
**GBIFOccurrenceTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GBIF_search_occurrences (from :doc:`gbif_tools`)
|
|
|
|
**GBIFTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GBIF_search_species (from :doc:`gbif_tools`)
|
|
|
|
**GDCCasesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GDC_search_cases (from :doc:`gdc_tools`)
|
|
|
|
**GDCFilesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GDC_list_files (from :doc:`gdc_tools`)
|
|
|
|
**GEOGetDatasetInfo** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* geo_get_dataset_info (from :doc:`geo_tools`)
|
|
|
|
**GEOGetSampleInfo** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* geo_get_sample_info (from :doc:`geo_tools`)
|
|
|
|
**GEOSearchDatasets** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* geo_search_datasets (from :doc:`geo_tools`)
|
|
|
|
**GINGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GIN_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**GTExEQTLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GTEx_query_eqtl (from :doc:`gtex_tools`)
|
|
|
|
**GTExExpressionTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GTEx_get_expression_summary (from :doc:`gtex_tools`)
|
|
|
|
**GWASAssociationByID** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_association_by_id (from :doc:`gwas_tools`)
|
|
|
|
**GWASAssociationSearch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_search_associations (from :doc:`gwas_tools`)
|
|
|
|
**GWASAssociationsForSNP** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_associations_for_snp (from :doc:`gwas_tools`)
|
|
|
|
**GWASAssociationsForStudy** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_associations_for_study (from :doc:`gwas_tools`)
|
|
|
|
**GWASAssociationsForTrait** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_associations_for_trait (from :doc:`gwas_tools`)
|
|
|
|
**GWASGeneSearch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GWAS_search_associations_by_gene (from :doc:`gwas_tools`)
|
|
|
|
**GWASSNPByID** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_snp_by_id (from :doc:`gwas_tools`)
|
|
|
|
**GWASSNPSearch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_search_snps (from :doc:`gwas_tools`)
|
|
|
|
**GWASSNPsForGene** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_snps_for_gene (from :doc:`gwas_tools`)
|
|
|
|
**GWASStudiesForTrait** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_studies_for_trait (from :doc:`gwas_tools`)
|
|
|
|
**GWASStudyByID** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_study_by_id (from :doc:`gwas_tools`)
|
|
|
|
**GWASStudySearch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_search_studies (from :doc:`gwas_tools`)
|
|
|
|
**GWASVariantsForTrait** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gwas_get_variants_for_trait (from :doc:`gwas_tools`)
|
|
|
|
**GeneOntologyTool** (5 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GO_get_annotations_for_gene (from :doc:`gene_ontology_tools`)
|
|
* GO_get_genes_for_term (from :doc:`gene_ontology_tools`)
|
|
* GO_get_term_by_id (from :doc:`gene_ontology_tools`)
|
|
* GO_get_term_details (from :doc:`gene_ontology_tools`)
|
|
* GO_search_terms (from :doc:`gene_ontology_tools`)
|
|
|
|
**GetSPLBySetIDTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* DailyMed_get_spl_by_setid (from :doc:`dailymed_tools`)
|
|
|
|
**GetToolInfo** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_tool_info (from :doc:`compact_mode_tools`)
|
|
|
|
**GrepTools** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* grep_tools (from :doc:`compact_mode_tools`)
|
|
|
|
**GtoPdbRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* GtoPdb_get_targets (from :doc:`gtopdb_tools`)
|
|
|
|
**HALTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HAL_search_archive (from :doc:`hal_tools`)
|
|
|
|
**HCATool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* hca_get_file_manifest (from :doc:`hca_tools`)
|
|
* hca_search_projects (from :doc:`hca_tools`)
|
|
|
|
**HPAGetBiologicalProcessTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_biological_processes_by_gene (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetCancerPrognosticsTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_cancer_prognostics_by_gene (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetComparativeExpressionTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_comparative_expression_by_gene_and_cellline (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetContextualBiologicalProcessTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_contextual_biological_process_analysis (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetDiseaseExpressionTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_disease_expression_by_gene_tissue_disease (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetGeneJSONTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_gene_basic_info_by_ensembl_id (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetGenePageDetailsTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_comprehensive_gene_details_by_ensembl_id (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetGeneXMLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_gene_tsv_data_by_ensembl_id (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetProteinInteractionsTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_protein_interactions_by_gene (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetRnaExpressionBySourceTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_rna_expression_by_source (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetRnaExpressionByTissueTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_rna_expression_in_specific_tissues (from :doc:`hpa_tools`)
|
|
|
|
**HPAGetSubcellularLocationTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_get_subcellular_location (from :doc:`hpa_tools`)
|
|
|
|
**HPASearchGenesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_search_genes_by_query (from :doc:`hpa_tools`)
|
|
|
|
**HPASearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* HPA_generic_search (from :doc:`hpa_tools`)
|
|
|
|
**HealthDisparitiesTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* health_disparities_get_county_rankings_info (from :doc:`health_disparities_tools`)
|
|
* health_disparities_get_svi_info (from :doc:`health_disparities_tools`)
|
|
|
|
**HumanBaseTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* humanbase_ppi_analysis (from :doc:`humanbase_tools`)
|
|
|
|
**IEDBTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* iedb_search_epitopes (from :doc:`iedb_tools`)
|
|
|
|
**InterProRESTTool** (3 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* InterPro_get_domain_details (from :doc:`interpro_tools`)
|
|
* InterPro_get_protein_domains (from :doc:`interpro_tools`)
|
|
* InterPro_search_domains (from :doc:`interpro_tools`)
|
|
|
|
**JASPARRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* JASPAR_get_transcription_factors (from :doc:`jaspar_tools`)
|
|
|
|
**KEGGFindGenes** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* kegg_find_genes (from :doc:`kegg_tools`)
|
|
|
|
**KEGGGetGeneInfo** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* kegg_get_gene_info (from :doc:`kegg_tools`)
|
|
|
|
**KEGGGetPathwayInfo** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* kegg_get_pathway_info (from :doc:`kegg_tools`)
|
|
|
|
**KEGGListOrganisms** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* kegg_list_organisms (from :doc:`kegg_tools`)
|
|
|
|
**KEGGSearchPathway** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* kegg_search_pathway (from :doc:`kegg_tools`)
|
|
|
|
**ListTools** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* list_tools (from :doc:`compact_mode_tools`)
|
|
|
|
**MCPAutoLoaderTool** (5 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* mcp_auto_loader_boltz (from :doc:`boltz_mcp_loader_tools`)
|
|
* mcp_auto_loader_expert_feedback (from :doc:`expert_feedback_tools`)
|
|
* mcp_auto_loader_server1 (from :doc:`mcp_client_tools_example`)
|
|
* mcp_auto_loader_txagent (from :doc:`txagent_client_tools`)
|
|
* mcp_auto_loader_uspto_downloader (from :doc:`uspto_downloader_tools`)
|
|
|
|
**MCPClientTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* mcp_client_example (from :doc:`mcp_client_tools_example`)
|
|
|
|
**MCPProxyTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* mcp_mock_calculator (from :doc:`mcp_client_tools_example`)
|
|
* mcp_mock_greeter (from :doc:`mcp_client_tools_example`)
|
|
|
|
**MGnifyAnalysesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* MGnify_list_analyses (from :doc:`mgnify_tools`)
|
|
|
|
**MGnifyStudiesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* MGnify_search_studies (from :doc:`mgnify_tools`)
|
|
|
|
**MPDRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* MPD_get_phenotype_data (from :doc:`mpd_tools`)
|
|
|
|
**MarkItDownTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* convert_to_markdown (from :doc:`markitdown_tools`)
|
|
|
|
**MedRxivTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* MedRxiv_search_preprints (from :doc:`medrxiv_tools`)
|
|
|
|
**MedlinePlusRESTTool** (5 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* MedlinePlus_connect_lookup_by_code (from :doc:`medlineplus_tools`)
|
|
* MedlinePlus_get_genetics_condition_by_name (from :doc:`medlineplus_tools`)
|
|
* MedlinePlus_get_genetics_gene_by_name (from :doc:`medlineplus_tools`)
|
|
* MedlinePlus_get_genetics_index (from :doc:`medlineplus_tools`)
|
|
* MedlinePlus_search_topics_by_keyword (from :doc:`medlineplus_tools`)
|
|
|
|
**Molecule2DTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* visualize_molecule_2d (from :doc:`molecule_2d_tools`)
|
|
|
|
**Molecule3DTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* visualize_molecule_3d (from :doc:`molecule_3d_tools`)
|
|
|
|
**Monarch** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_HPO_ID_by_phenotype (from :doc:`monarch_tools`)
|
|
* get_phenotype_by_HPO_ID (from :doc:`monarch_tools`)
|
|
|
|
**MonarchDiseasesForMultiplePheno** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_joint_associated_diseases_by_HPO_ID_list (from :doc:`monarch_tools`)
|
|
|
|
**NCBIBlastTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* BLAST_nucleotide_search (from :doc:`blast_tools`)
|
|
* BLAST_protein_search (from :doc:`blast_tools`)
|
|
|
|
**NHANESTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* nhanes_get_dataset_info (from :doc:`nhanes_tools`)
|
|
* nhanes_search_datasets (from :doc:`nhanes_tools`)
|
|
|
|
**NICEGuidelineFullTextTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* NICE_Guideline_Full_Text (from :doc:`unified_guideline_tools`)
|
|
|
|
**NICEWebScrapingTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* NICE_Clinical_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**OBISOccurrenceTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OBIS_search_occurrences (from :doc:`obis_tools`)
|
|
|
|
**OBISTaxaTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OBIS_search_taxa (from :doc:`obis_tools`)
|
|
|
|
**ODPHPItemList** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* odphp_itemlist (from :doc:`odphp_tools`)
|
|
|
|
**ODPHPMyHealthfinder** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* odphp_myhealthfinder (from :doc:`odphp_tools`)
|
|
|
|
**ODPHPOutlinkFetch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* odphp_outlink_fetch (from :doc:`odphp_tools`)
|
|
|
|
**ODPHPTopicSearch** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* odphp_topicsearch (from :doc:`odphp_tools`)
|
|
|
|
**OLSTool** (7 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ols_find_similar_terms (from :doc:`ols_tools`)
|
|
* ols_get_ontology_info (from :doc:`ols_tools`)
|
|
* ols_get_term_ancestors (from :doc:`ols_tools`)
|
|
* ols_get_term_children (from :doc:`ols_tools`)
|
|
* ols_get_term_info (from :doc:`ols_tools`)
|
|
* ols_search_ontologies (from :doc:`ols_tools`)
|
|
* ols_search_terms (from :doc:`ols_tools`)
|
|
|
|
**OSFPreprintsTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OSF_search_preprints (from :doc:`osf_preprints_tools`)
|
|
|
|
**OpenAIRETool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OpenAIRE_search_publications (from :doc:`openaire_tools`)
|
|
|
|
**OpenAlexGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OpenAlex_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**OpenAlexTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* openalex_literature_search (from :doc:`openalex_tools`)
|
|
|
|
**OpenTarget** (55 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OpenTargets_drug_pharmacogenomics_data (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_approved_indications_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_diseases_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_drugs_by_disease_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_drugs_by_target_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_phenotypes_by_disease_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_targets_by_disease_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_associated_targets_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_biological_mouse_models_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_chemical_probes_by_target_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_ancestors_parents_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_descendants_children_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_description_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_id_description_by_name (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_ids_by_efoId (from :doc:`idmap_tools`)
|
|
* OpenTargets_get_disease_ids_by_name (from :doc:`idmap_tools`)
|
|
* OpenTargets_get_disease_locations_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_synonyms_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_disease_therapeutic_areas_by_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_diseases_phenotypes_by_target_ensembl (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_adverse_events_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_approval_status_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_description_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_indications_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_mechanisms_of_action_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_names_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_synonyms_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_trade_names_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_warnings_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_gene_ontology_terms_by_goID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_known_drugs_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_parent_child_molecules_by_drug_chembl_ID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_publications_by_disease_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_publications_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_publications_by_target_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_similar_entities_by_disease_efoId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_similar_entities_by_drug_chemblId (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_similar_entities_by_target_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_classes_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_constraint_info_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_enabling_packages_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_gene_ontology_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_genomic_location_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_homologues_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_id_description_by_name (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_interactions_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_safety_profile_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_subcellular_locations_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_synonyms_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_target_tractability_by_ensemblID (from :doc:`opentarget_tools`)
|
|
* OpenTargets_map_any_disease_id_to_all_other_ids (from :doc:`idmap_tools`)
|
|
* OpenTargets_multi_entity_search_by_query_string (from :doc:`opentarget_tools`)
|
|
* OpenTargets_search_category_counts_by_query_string (from :doc:`opentarget_tools`)
|
|
* OpenTargets_target_disease_evidence (from :doc:`opentarget_tools`)
|
|
|
|
**OpentargetToolDrugNameMatch** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* OpenTargets_get_drug_chembId_by_generic_name (from :doc:`opentarget_tools`)
|
|
* OpenTargets_get_drug_id_description_by_name (from :doc:`opentarget_tools`)
|
|
|
|
**PMCTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PMC_search_papers (from :doc:`pmc_tools`)
|
|
|
|
**PRIDERESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PRIDE_search_proteomics (from :doc:`pride_tools`)
|
|
|
|
**PackageTool** (163 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_albumentations_info (from :doc:`image_processing_tools`)
|
|
* get_altair_info (from :doc:`visualization_tools`)
|
|
* get_anndata_info (from :doc:`single_cell_tools`)
|
|
* get_arboreto_info (from :doc:`genomics_tools`)
|
|
* get_arxiv_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_ase_info (from :doc:`structural_biology_tools`)
|
|
* get_astropy_info (from :doc:`physics_astronomy_tools`)
|
|
* get_biopandas_info (from :doc:`structural_biology_tools`)
|
|
* get_biopython_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_bioservices_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_biotite_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_bokeh_info (from :doc:`visualization_tools`)
|
|
* get_brian2_info (from :doc:`neuroscience_tools`)
|
|
* get_cartopy_info (from :doc:`earth_sciences_tools`)
|
|
* get_catboost_info (from :doc:`machine_learning_tools`)
|
|
* get_cellpose_info (from :doc:`visualization_tools`)
|
|
* get_cellrank_info (from :doc:`single_cell_tools`)
|
|
* get_cellxgene_census_info (from :doc:`genomics_tools`)
|
|
* get_cftime_info (from :doc:`earth_sciences_tools`)
|
|
* get_chembl_webresource_client_info (from :doc:`cheminformatics_tools`)
|
|
* get_clair3_info (from :doc:`genomics_tools`)
|
|
* get_cobra_info (from :doc:`cheminformatics_tools`)
|
|
* get_cobrapy_info (from :doc:`machine_learning_tools`)
|
|
* get_cooler_info (from :doc:`scientific_computing_tools`)
|
|
* get_cryosparc_tools_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_cupy_info (from :doc:`scientific_computing_tools`)
|
|
* get_cyvcf2_info (from :doc:`genomics_tools`)
|
|
* get_dask_info (from :doc:`scientific_computing_tools`)
|
|
* get_datamol_info (from :doc:`cheminformatics_tools`)
|
|
* get_datashader_info (from :doc:`visualization_tools`)
|
|
* get_deepchem_info (from :doc:`cheminformatics_tools`)
|
|
* get_deeppurpose_info (from :doc:`machine_learning_tools`)
|
|
* get_deeptools_info (from :doc:`genomics_tools`)
|
|
* get_deepxde_info (from :doc:`machine_learning_tools`)
|
|
* get_dendropy_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_descriptastorus_info (from :doc:`structural_biology_tools`)
|
|
* get_diffdock_info (from :doc:`structural_biology_tools`)
|
|
* get_dscribe_info (from :doc:`cheminformatics_tools`)
|
|
* get_elephant_info (from :doc:`neuroscience_tools`)
|
|
* get_episcanpy_info (from :doc:`single_cell_tools`)
|
|
* get_ete3_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_faiss_info (from :doc:`machine_learning_tools`)
|
|
* get_fanc_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_flask_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_flowio_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_flowkit_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_flowutils_info (from :doc:`scientific_computing_tools`)
|
|
* get_freesasa_info (from :doc:`structural_biology_tools`)
|
|
* get_galpy_info (from :doc:`physics_astronomy_tools`)
|
|
* get_geopandas_info (from :doc:`earth_sciences_tools`)
|
|
* get_gget_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_googlesearch_python_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_gseapy_info (from :doc:`genomics_tools`)
|
|
* get_h5py_info (from :doc:`scientific_computing_tools`)
|
|
* get_harmony_pytorch_info (from :doc:`machine_learning_tools`)
|
|
* get_hmmlearn_info (from :doc:`machine_learning_tools`)
|
|
* get_holoviews_info (from :doc:`visualization_tools`)
|
|
* get_htmd_info (from :doc:`structural_biology_tools`)
|
|
* get_igraph_info (from :doc:`visualization_tools`)
|
|
* get_imageio_info (from :doc:`image_processing_tools`)
|
|
* get_imbalanced_learn_info (from :doc:`machine_learning_tools`)
|
|
* get_jcvi_info (from :doc:`genomics_tools`)
|
|
* get_joblib_info (from :doc:`scientific_computing_tools`)
|
|
* get_khmer_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_kipoiseq_info (from :doc:`genomics_tools`)
|
|
* get_lifelines_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_lightgbm_info (from :doc:`machine_learning_tools`)
|
|
* get_loompy_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_mageck_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_matplotlib_info (from :doc:`visualization_tools`)
|
|
* get_mdanalysis_info (from :doc:`structural_biology_tools`)
|
|
* get_mdtraj_info (from :doc:`structural_biology_tools`)
|
|
* get_mne_info (from :doc:`neuroscience_tools`)
|
|
* get_molfeat_info (from :doc:`cheminformatics_tools`)
|
|
* get_molvs_info (from :doc:`cheminformatics_tools`)
|
|
* get_mordred_info (from :doc:`cheminformatics_tools`)
|
|
* get_msprime_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_mudata_info (from :doc:`single_cell_tools`)
|
|
* get_neo_info (from :doc:`neuroscience_tools`)
|
|
* get_netcdf4_info (from :doc:`earth_sciences_tools`)
|
|
* get_networkx_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_nglview_info (from :doc:`structural_biology_tools`)
|
|
* get_nilearn_info (from :doc:`neuroscience_tools`)
|
|
* get_numba_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_numpy_info (from :doc:`scientific_computing_tools`)
|
|
* get_openbabel_info (from :doc:`cheminformatics_tools`)
|
|
* get_openchem_info (from :doc:`cheminformatics_tools`)
|
|
* get_opencv_info (from :doc:`visualization_tools`)
|
|
* get_openmm_info (from :doc:`structural_biology_tools`)
|
|
* get_optlang_info (from :doc:`scientific_computing_tools`)
|
|
* get_optuna_info (from :doc:`machine_learning_tools`)
|
|
* get_palantir_info (from :doc:`single_cell_tools`)
|
|
* get_pandas_info (from :doc:`scientific_computing_tools`)
|
|
* get_patsy_info (from :doc:`scientific_computing_tools`)
|
|
* get_pdbfixer_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pillow_info (from :doc:`image_processing_tools`)
|
|
* get_plantcv_info (from :doc:`visualization_tools`)
|
|
* get_plip_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_plotly_info (from :doc:`visualization_tools`)
|
|
* get_poliastro_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_poretools_info (from :doc:`genomics_tools`)
|
|
* get_prody_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pubchempy_info (from :doc:`cheminformatics_tools`)
|
|
* get_pybedtools_info (from :doc:`genomics_tools`)
|
|
* get_pybigwig_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pydeseq2_info (from :doc:`genomics_tools`)
|
|
* get_pyensembl_info (from :doc:`genomics_tools`)
|
|
* get_pyephem_info (from :doc:`physics_astronomy_tools`)
|
|
* get_pyfaidx_info (from :doc:`genomics_tools`)
|
|
* get_pyfasta_info (from :doc:`genomics_tools`)
|
|
* get_pykalman_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pyliftover_info (from :doc:`genomics_tools`)
|
|
* get_pymassspec_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pymed_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pymzml_info (from :doc:`machine_learning_tools`)
|
|
* get_pypdf2_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pyranges_info (from :doc:`genomics_tools`)
|
|
* get_pyrosetta_info (from :doc:`structural_biology_tools`)
|
|
* get_pysam_info (from :doc:`genomics_tools`)
|
|
* get_pyscenic_info (from :doc:`single_cell_tools`)
|
|
* get_pyscf_info (from :doc:`structural_biology_tools`)
|
|
* get_pyscreener_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_pytdc_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_python_libsbml_info (from :doc:`machine_learning_tools`)
|
|
* get_pytorch_info (from :doc:`machine_learning_tools`)
|
|
* get_pyvcf_info (from :doc:`genomics_tools`)
|
|
* get_pyvis_info (from :doc:`visualization_tools`)
|
|
* get_qutip_info (from :doc:`physics_astronomy_tools`)
|
|
* get_rasterio_info (from :doc:`earth_sciences_tools`)
|
|
* get_rdkit_info (from :doc:`cheminformatics_tools`)
|
|
* get_reportlab_info (from :doc:`genomics_tools`)
|
|
* get_requests_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_ruptures_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_scanorama_info (from :doc:`single_cell_tools`)
|
|
* get_scanpy_info (from :doc:`single_cell_tools`)
|
|
* get_schnetpack_info (from :doc:`machine_learning_tools`)
|
|
* get_scholarly_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_scikit_bio_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_scikit_image_info (from :doc:`visualization_tools`)
|
|
* get_scikit_learn_info (from :doc:`machine_learning_tools`)
|
|
* get_scipy_info (from :doc:`scientific_computing_tools`)
|
|
* get_scrublet_info (from :doc:`single_cell_tools`)
|
|
* get_scvelo_info (from :doc:`single_cell_tools`)
|
|
* get_scvi_tools_info (from :doc:`single_cell_tools`)
|
|
* get_seaborn_info (from :doc:`visualization_tools`)
|
|
* get_skopt_info (from :doc:`machine_learning_tools`)
|
|
* get_souporcell_info (from :doc:`single_cell_tools`)
|
|
* get_statsmodels_info (from :doc:`machine_learning_tools`)
|
|
* get_sunpy_info (from :doc:`physics_astronomy_tools`)
|
|
* get_sympy_info (from :doc:`scientific_computing_tools`)
|
|
* get_tiledb_info (from :doc:`scientific_computing_tools`)
|
|
* get_tiledbsoma_info (from :doc:`single_cell_tools`)
|
|
* get_torch_geometric_info (from :doc:`machine_learning_tools`)
|
|
* get_tqdm_info (from :doc:`scientific_computing_tools`)
|
|
* get_trackpy_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_tskit_info (from :doc:`bioinformatics_core_tools`)
|
|
* get_umap_learn_info (from :doc:`machine_learning_tools`)
|
|
* get_velocyto_info (from :doc:`single_cell_tools`)
|
|
* get_viennarna_info (from :doc:`genomics_tools`)
|
|
* get_xarray_info (from :doc:`scientific_computing_tools`)
|
|
* get_xesmf_info (from :doc:`earth_sciences_tools`)
|
|
* get_xgboost_info (from :doc:`machine_learning_tools`)
|
|
* get_zarr_info (from :doc:`scientific_computing_tools`)
|
|
|
|
**PaleobiologyRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Paleobiology_get_fossils (from :doc:`paleobiology_tools`)
|
|
|
|
**PathwayCommonsTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* pc_get_interactions (from :doc:`pathway_commons_tools`)
|
|
* pc_search_pathways (from :doc:`pathway_commons_tools`)
|
|
|
|
**ProteinStructure3DTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* visualize_protein_structure_3d (from :doc:`protein_structure_3d_tools`)
|
|
|
|
**PubChemRESTTool** (9 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PubChem_get_CID_by_SMILES (from :doc:`pubchem_tools`)
|
|
* PubChem_get_CID_by_compound_name (from :doc:`pubchem_tools`)
|
|
* PubChem_get_associated_patents_by_CID (from :doc:`pubchem_tools`)
|
|
* PubChem_get_compound_2D_image_by_CID (from :doc:`pubchem_tools`)
|
|
* PubChem_get_compound_properties_by_CID (from :doc:`pubchem_tools`)
|
|
* PubChem_get_compound_synonyms_by_CID (from :doc:`pubchem_tools`)
|
|
* PubChem_get_compound_xrefs_by_CID (from :doc:`pubchem_tools`)
|
|
* PubChem_search_compounds_by_similarity (from :doc:`pubchem_tools`)
|
|
* PubChem_search_compounds_by_substructure (from :doc:`pubchem_tools`)
|
|
|
|
**PubMedGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PubMed_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**PubMedTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PubMed_search_articles (from :doc:`pubmed_tools`)
|
|
|
|
**PubTatorTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PubTator3_EntityAutocomplete (from :doc:`pubtator_tools`)
|
|
* PubTator3_LiteratureSearch (from :doc:`pubtator_tools`)
|
|
|
|
**PyPIPackageInspector** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PyPIPackageInspector (from :doc:`pypi_package_inspector_tools`)
|
|
|
|
**PythonCodeExecutor** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* python_code_executor (from :doc:`python_executor_tools`)
|
|
|
|
**PythonScriptRunner** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* python_script_runner (from :doc:`python_executor_tools`)
|
|
|
|
**RCSBSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* PDB_search_similar_structures (from :doc:`rcsb_search_tools`)
|
|
|
|
**RCSBTool** (39 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_assembly_info_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_assembly_summary (from :doc:`rcsb_pdb_tools`)
|
|
* get_binding_affinity_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_chem_comp_audit_info (from :doc:`rcsb_pdb_tools`)
|
|
* get_chem_comp_charge_and_ambiguity (from :doc:`rcsb_pdb_tools`)
|
|
* get_citation_info_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_core_refinement_statistics (from :doc:`rcsb_pdb_tools`)
|
|
* get_crystal_growth_conditions_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_crystallization_ph_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_crystallographic_properties_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_ec_number_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_em_3d_fitting_and_reconstruction_details (from :doc:`rcsb_pdb_tools`)
|
|
* get_emdb_ids_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_gene_name_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_host_organism_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_ligand_bond_count_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_ligand_smiles_by_chem_comp_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_mutation_annotations_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_oligosaccharide_descriptors_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_polymer_entity_annotations (from :doc:`rcsb_pdb_tools`)
|
|
* get_polymer_entity_count_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_polymer_entity_ids_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_polymer_entity_type_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_polymer_molecular_weight_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_protein_classification_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_protein_metadata_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_refinement_resolution_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_release_deposit_dates_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_sequence_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_sequence_lengths_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_sequence_positional_features_by_instance_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_source_organism_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_space_group_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_structure_determination_software_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_structure_title_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_structure_validation_metrics_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_target_cofactor_info (from :doc:`rcsb_pdb_tools`)
|
|
* get_taxonomy_by_pdb_id (from :doc:`rcsb_pdb_tools`)
|
|
* get_uniprot_accession_by_entity_id (from :doc:`rcsb_pdb_tools`)
|
|
|
|
**RNAcentralGetTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* RNAcentral_get_by_accession (from :doc:`rnacentral_tools`)
|
|
|
|
**RNAcentralSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* RNAcentral_search (from :doc:`rnacentral_tools`)
|
|
|
|
**ReMapRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* ReMap_get_transcription_factor_binding (from :doc:`remap_tools`)
|
|
|
|
**ReactomeRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Reactome_get_pathway_reactions (from :doc:`reactome_tools`)
|
|
|
|
**RegulomeDBRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* RegulomeDB_query_variant (from :doc:`regulomedb_tools`)
|
|
|
|
**RemoteTool** (14 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Remote Tools:*
|
|
* boltz2_docking (from :doc:`boltz_tools`)
|
|
* compute_depmap24q2_gene_correlations (from :doc:`depmap_tools`)
|
|
* consult_human_expert (from :doc:`expert_feedback_tools`)
|
|
* get_abstract_from_patent_app_number (from :doc:`uspto_downloader_tools`)
|
|
* get_claims_from_patent_app_number (from :doc:`uspto_downloader_tools`)
|
|
* get_expert_response (from :doc:`expert_feedback_tools`)
|
|
* get_expert_status (from :doc:`expert_feedback_tools`)
|
|
* get_full_text_from_patent_app_number (from :doc:`uspto_downloader_tools`)
|
|
* list_pending_expert_requests (from :doc:`expert_feedback_tools`)
|
|
* mcp_auto_loader_human_expert (from :doc:`expert_feedback_tools`)
|
|
* run_compass_prediction (from :doc:`immune_compass_tools`)
|
|
* run_pinnacle_ppi_retrieval (from :doc:`pinnacle_tools`)
|
|
* run_transcriptformer_embedding_retrieval (from :doc:`transcriptformer_tools`)
|
|
* submit_expert_response (from :doc:`expert_feedback_tools`)
|
|
|
|
**RxNormTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* RxNorm_get_drug_names (from :doc:`rxnorm_tools`)
|
|
|
|
**SCREENRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* SCREEN_get_regulatory_elements (from :doc:`screen_tools`)
|
|
|
|
**STRINGRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* STRING_get_protein_interactions (from :doc:`ppi_tools`)
|
|
|
|
**SearchSPLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* DailyMed_search_spls (from :doc:`dailymed_tools`)
|
|
|
|
**SemanticScholarTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* SemanticScholar_search_papers (from :doc:`semantic_scholar_tools`)
|
|
|
|
**SmolAgentTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* advanced_literature_search_agent (from :doc:`smolagent_tools`)
|
|
* open_deep_research_agent (from :doc:`smolagent_tools`)
|
|
|
|
**SpecialTool** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* CallAgent (from :doc:`special_tools`)
|
|
* Finish (from :doc:`special_tools`)
|
|
|
|
**TRIPDatabaseTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* TRIP_Database_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**TextDownloadTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* download_text_content (from :doc:`file_download_tools`)
|
|
|
|
**ToolFinderEmbedding** (2 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Tool_Finder (from :doc:`finder_tools`)
|
|
* Tool_RAG (from :doc:`finder_tools`)
|
|
|
|
**ToolFinderKeyword** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Tool_Finder_Keyword (from :doc:`finder_tools`)
|
|
|
|
**ToolFinderLLM** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Tool_Finder_LLM (from :doc:`finder_tools`)
|
|
|
|
**UMLSRESTTool** (5 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* icd_search_codes (from :doc:`umls_tools`)
|
|
* loinc_search_codes (from :doc:`umls_tools`)
|
|
* snomed_search_concepts (from :doc:`umls_tools`)
|
|
* umls_get_concept_details (from :doc:`umls_tools`)
|
|
* umls_search_concepts (from :doc:`umls_tools`)
|
|
|
|
**URLHTMLTagTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_webpage_title (from :doc:`url_fetch_tools`)
|
|
|
|
**URLToPDFTextTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_webpage_text_from_url (from :doc:`url_fetch_tools`)
|
|
|
|
**USPTOOpenDataPortalTool** (6 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* get_associated_documents_metadata (from :doc:`uspto_tools`)
|
|
* get_patent_application_metadata (from :doc:`uspto_tools`)
|
|
* get_patent_continuity_data (from :doc:`uspto_tools`)
|
|
* get_patent_foreign_priority_data (from :doc:`uspto_tools`)
|
|
* get_patent_overview_by_text_query (from :doc:`uspto_tools`)
|
|
* get_patent_term_adjustment_data (from :doc:`uspto_tools`)
|
|
|
|
**UniProtRESTTool** (12 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* UniProt_get_alternative_names_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_disease_variants_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_entry_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_function_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_isoform_ids_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_organism_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_ptm_processing_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_recommended_name_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_sequence_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_get_subcellular_location_by_accession (from :doc:`uniprot_tools`)
|
|
* UniProt_id_mapping (from :doc:`uniprot_tools`)
|
|
* UniProt_search (from :doc:`uniprot_tools`)
|
|
|
|
**UnpaywallTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Unpaywall_check_oa_status (from :doc:`unpaywall_tools`)
|
|
|
|
**WHOGHOQueryTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* who_gho_query_health_data (from :doc:`who_gho_tools`)
|
|
|
|
**WHOGHORESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* who_gho_get_data (from :doc:`who_gho_tools`)
|
|
|
|
**WHOGuidelineFullTextTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* WHO_Guideline_Full_Text (from :doc:`unified_guideline_tools`)
|
|
|
|
**WHOGuidelinesTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* WHO_Guidelines_Search (from :doc:`unified_guideline_tools`)
|
|
|
|
**WebAPIDocumentationSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* web_api_documentation_search (from :doc:`web_search_tools`)
|
|
|
|
**WebSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* web_search (from :doc:`web_search_tools`)
|
|
|
|
**WikiPathwaysGetTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* WikiPathways_get_pathway (from :doc:`wikipathways_tools`)
|
|
|
|
**WikiPathwaysSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* WikiPathways_search (from :doc:`wikipathways_tools`)
|
|
|
|
**WikidataSPARQLTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Wikidata_SPARQL_query (from :doc:`wikidata_sparql_tools`)
|
|
|
|
**WikipediaContentTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Wikipedia_get_content (from :doc:`wikipedia_tools`)
|
|
|
|
**WikipediaSearchTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Wikipedia_search (from :doc:`wikipedia_tools`)
|
|
|
|
**WikipediaSummaryTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Wikipedia_get_summary (from :doc:`wikipedia_tools`)
|
|
|
|
**WoRMSRESTTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* WoRMS_search_species (from :doc:`worms_tools`)
|
|
|
|
**XMLTool** (19 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* drugbank_filter_drugs_by_name (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_desc_pharmacology_by_moa (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_interactions_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_name_and_description_by_indication (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_name_and_description_by_pathway_name (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_name_and_description_by_target_name (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_products_by_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_drug_references_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_indications_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_pathways_reactions_by_drug_or_id (from :doc:`xml_tools`)
|
|
* drugbank_get_pharmacology_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_safety_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* drugbank_get_targets_by_drug_name_or_drugbank_id (from :doc:`xml_tools`)
|
|
* mesh_get_subjects_by_pharmacological_action (from :doc:`xml_tools`)
|
|
* mesh_get_subjects_by_subject_id (from :doc:`xml_tools`)
|
|
* mesh_get_subjects_by_subject_name (from :doc:`xml_tools`)
|
|
* mesh_get_subjects_by_subject_scope_or_definition (from :doc:`xml_tools`)
|
|
|
|
**ZenodoTool** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* Zenodo_search_records (from :doc:`zenodo_tools`)
|
|
|
|
**dbSNPGetFrequencies** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* dbsnp_get_frequencies (from :doc:`dbsnp_tools`)
|
|
|
|
**dbSNPGetVariantByRsID** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* dbsnp_get_variant_by_rsid (from :doc:`dbsnp_tools`)
|
|
|
|
**dbSNPSearchByGene** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* dbsnp_search_by_gene (from :doc:`dbsnp_tools`)
|
|
|
|
**gnomADGetGeneConstraints** (1 tools)
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
*Local Tools:*
|
|
* gnomad_get_gene_constraints (from :doc:`gnomad_tools`)
|
|
|
|
|
|
Quick Tool Search
|
|
-----------------
|
|
|
|
Use your browser's search function (Ctrl+F / Cmd+F) to quickly find:
|
|
|
|
* **Tool Name**: Search for the exact tool name
|
|
* **File Path**: Search for ``filename.json`` to find all tools in that file
|
|
* **Tool Type**: Search for specific tool types like "AgenticTool", "OpenTarget", etc.
|
|
|
|
.. note::
|
|
Each configuration file has its own dedicated page with detailed tool information and collapsible sections.
|
|
|