biocatalystfeed 0.2.0__tar.gz

biocatalystfeed-0.2.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

biocatalystfeed-0.2.0/NOTICE

@@ -0,0 +1,26 @@
+BioCatalystFeed
+Copyright 2026 The BioCatalystFeed authors
+
+This product is licensed under the Apache License, Version 2.0 (see LICENSE).
+
+BioCatalystFeed is an independent open-source project. It is not affiliated with, endorsed by, or sponsored by any of
+the agencies or services below. Their names are used only to identify the source of data.
+
+Data sources and attributions
+-----------------------------
+- ClinicalTrials.gov, U.S. National Library of Medicine (NLM), National Institutes of Health. Data retrieved via the
+  ClinicalTrials.gov API v2. NLM does not endorse this product. Some records may reference third-party rights.
+- Data provided by the U.S. Food and Drug Administration (https://open.fda.gov). openFDA data is not validated for
+  clinical or production use; do not rely on it for medical decisions.
+- NIH RePORTER, National Institutes of Health (https://reporter.nih.gov). U.S. federal award data.
+- PubMed / NCBI E-utilities, U.S. National Library of Medicine. Citations are retrieved as metadata; abstracts may be
+  subject to publisher copyright and are not stored or redistributed by this software.
+- Europe PMC (https://europepmc.org), via the Europe PMC RESTful Web Service. Metadata and links only.
+- bioRxiv and medRxiv preprint servers (https://www.biorxiv.org, https://www.medrxiv.org), via api.biorxiv.org and via
+  Europe PMC. Each preprint carries its own licence; this software keeps metadata and links only.
+- SEC EDGAR, U.S. Securities and Exchange Commission. Public filing data accessed under the SEC fair-access policy.
+
+Disclaimer
+----------
+Not investment, legal or medical advice. Data may be incomplete, delayed or wrong; PDUFA dates are unverified
+candidates extracted from SEC filings.

biocatalystfeed-0.2.0/PKG-INFO

@@ -0,0 +1,107 @@
+Metadata-Version: 2.4
+Name: biocatalystfeed
+Version: 0.2.0
+Summary: Open-source monitors for biotech catalysts: ClinicalTrials.gov, openFDA, NIH RePORTER, PubMed/Europe PMC/bioRxiv, SEC EDGAR. CLI + MCP server.
+License-Expression: Apache-2.0
+Keywords: biotech,clinical-trials,fda,pubmed,mcp,sec-edgar,monitoring
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: requests>=2.28
+Provides-Extra: mcp
+Requires-Dist: mcp>=1.2; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Dynamic: license-file
+
+# BioCatalystFeed
+
+**An open-source catalyst feed for biotech: see what changed across clinical trials, FDA actions, NIH grants,
+papers/preprints and SEC filings for the companies and drugs you follow.** Use it as a CLI, as an MCP server for AI
+agents (Claude, Cursor, …), or as an Apify actor.
+
+> ⚠️ **Not investment, legal or medical advice.** Data may be incomplete, delayed or wrong; PDUFA dates are unverified
+> candidates from SEC filings. Always check the linked primary source.
+
+## What it does
+| Source | Command | What you get |
+|---|---|---|
+| ClinicalTrials.gov API v2 (NLM) | `bcf trials` | search, sponsor pipelines, **diffs**: new trials, status/phase/enrollment/date changes |
+| openFDA (Drugs@FDA, SPL labels) | `bcf fda` | approvals (incl. novel NME/BLA flag), submissions, label revisions, diffs |
+| NIH RePORTER | `bcf grants` | grants by org / PI (middle-initial aware) / keyword; new awards, amount changes |
+| PubMed + **Europe PMC** + bioRxiv/medRxiv | `bcf papers` | papers & preprints, **deduplicated by DOI/PMID** across sources |
+| SEC EDGAR | `bcf sec` | 8-K mentions of PDUFA dates (UNVERIFIED candidates, linked to the filing) |
+| All of the above | `bcf profile` | one merged company profile (name or ticker) |
+
+Across tools: `--exclude TERM …` to drop noise, `--rank` for relevance ordering, and `--rss` / `--json-feed` digest
+files on every `watch` (local files you can serve or feed into any reader; nothing is emailed).
+
+## Quickstart
+```bash
+python3 -m venv .venv && .venv/bin/pip install -e '.[mcp]'     # PyPI package: not yet published
+source .venv/bin/activate
+
+bcf trials search --sponsor "Viking Therapeutics" --phase PHASE3
+bcf papers search --drug resmetirom --since 2026-09-01 --exclude mice rat --rank
+bcf grants search --pi "Ioannou, George N" --since 2024-01-01 --no-future
+bcf sec pdufa MDGL --since 2023-01-01
+bcf profile Lilly MDGL "Viking Therapeutics" --md profiles.md
+
+# watches: first run = baseline, later runs report what changed (cron it daily)
+bcf trials --db bcf.db watch --name obesity --condition obesity --phase PHASE3 --rss obesity.rss
+bcf papers --db bcf.db watch --name mdgl --affiliation "Madrigal Pharmaceuticals" --json-feed mdgl.feed.json
+```
+The old commands (`trialwatch`, `fdawatch`, `grantwatch`, `paperwatch`, `secwatch`, `trialwatch-mcp`) still work.
+
+### MCP server
+```json
+{"mcpServers": {"biocatalystfeed": {"command": "/path/to/.venv/bin/biocatalystfeed-mcp",
+  "env": {"BIOCATALYSTFEED_DB": "/path/to/bcf.db"}}}}
+```
+Tools include `search_trials`, `sponsor_pipeline`, `fda_approvals`, `company_profile`, `search_grants`,
+`search_papers`, `sec_pdufa_mentions`, `snapshot_*` / `*_changes_since`, and `changes_feed` (RSS / JSON Feed).
+
+### Configuration
+| Env var | Purpose |
+|---|---|
+| `BIOCATALYSTFEED_CONTACT` | contact email put in the SEC User-Agent (SEC fair-access policy). Default is a placeholder (`contact@biocatalystfeed.invalid`); **set it to your own contact before heavy SEC use** |
+| `SEC_USER_AGENT` | full SEC User-Agent override |
+| `NCBI_EMAIL` | optional email sent to NCBI E-utilities |
+| `BIOCATALYSTFEED_DB` (or `TRIALWATCH_DB`) | SQLite DB for the MCP server |
+| `FDAWATCH_ALIASES` | JSON file extending the company alias table |
+
+## How it compares
+Facts about DataLookout are from datalookout.com/citeline-alternative (checked 2026-10-12 PT). We have not tested
+their product.
+
+| | BioCatalystFeed (open source) | DataLookout |
+|---|---|---|
+| Price | Free (Apache-2.0); hosted tier planned | Free tier; Pro $49/month |
+| Sources | ClinicalTrials.gov, openFDA, NIH RePORTER, PubMed, Europe PMC, bioRxiv/medRxiv, SEC EDGAR | ClinicalTrials.gov |
+| Change tracking | Diffs between your own runs (trials: status, phase, enrollment, dates, sponsor, title, why stopped, results; plus FDA, grant, paper and SEC changes) | Daily scan; 13 fields incl. status, enrollment, primary endpoints, interventions, results, site counts, completion dates; changes marked Stopped/Notable/Minor |
+| Delivery | CLI, MCP server for AI agents, RSS/JSON Feed files, Apify actor | Morning email digest + dashboard inbox |
+| Watch limits | None when self-hosted | Free: 1 sponsor + 1 disease watchlist + 1 saved search; Pro: 10 of each |
+| Scheduling | You run it (cron, Apify schedule) | Hosted, daily |
+| Setup | Python install | "2 minutes" (their claim) |
+
+Pick DataLookout for a hosted, emailed, ClinicalTrials.gov-only digest. Pick BioCatalystFeed if you want several
+sources per company or ticker, agent/MCP access, or to self-host.
+
+## Data sources, limits and etiquette
+Built-in throttles follow each source's published policy (e.g. NIH RePORTER 1 req/s, NCBI ≤3 req/s without key, SEC
+≤10 req/s with a declared User-Agent, openFDA 1,000 req/day per IP without key). We store **metadata and links only**
+for papers/preprints, never abstracts. Change detection only covers your own runs; there's no historical backfill.
+PDUFA dates are regex extractions from 8-K text, not a calendar. Attributions are in [`NOTICE`](NOTICE). Design notes
+and per-source terms are in [`docs/DEVELOPER-NOTES.md`](docs/DEVELOPER-NOTES.md).
+
+## Hosted tier
+A paid hosted version (scheduled watches, persisted history, hosted MCP) is planned. Draft terms:
+[`TERMS.md`](TERMS.md), [`PRIVACY.md`](PRIVACY.md) (drafts, not legal advice, not in effect).
+
+## Contributing & licence
+See [`CONTRIBUTING.md`](CONTRIBUTING.md). Licensed under the [Apache License 2.0](LICENSE). BioCatalystFeed is
+independent and not endorsed by NLM, NIH, FDA, SEC, EMBL-EBI/Europe PMC, or bioRxiv/medRxiv.

biocatalystfeed-0.2.0/README.md

@@ -0,0 +1,87 @@
+# BioCatalystFeed
+
+**An open-source catalyst feed for biotech: see what changed across clinical trials, FDA actions, NIH grants,
+papers/preprints and SEC filings for the companies and drugs you follow.** Use it as a CLI, as an MCP server for AI
+agents (Claude, Cursor, …), or as an Apify actor.
+
+> ⚠️ **Not investment, legal or medical advice.** Data may be incomplete, delayed or wrong; PDUFA dates are unverified
+> candidates from SEC filings. Always check the linked primary source.
+
+## What it does
+| Source | Command | What you get |
+|---|---|---|
+| ClinicalTrials.gov API v2 (NLM) | `bcf trials` | search, sponsor pipelines, **diffs**: new trials, status/phase/enrollment/date changes |
+| openFDA (Drugs@FDA, SPL labels) | `bcf fda` | approvals (incl. novel NME/BLA flag), submissions, label revisions, diffs |
+| NIH RePORTER | `bcf grants` | grants by org / PI (middle-initial aware) / keyword; new awards, amount changes |
+| PubMed + **Europe PMC** + bioRxiv/medRxiv | `bcf papers` | papers & preprints, **deduplicated by DOI/PMID** across sources |
+| SEC EDGAR | `bcf sec` | 8-K mentions of PDUFA dates (UNVERIFIED candidates, linked to the filing) |
+| All of the above | `bcf profile` | one merged company profile (name or ticker) |
+
+Across tools: `--exclude TERM …` to drop noise, `--rank` for relevance ordering, and `--rss` / `--json-feed` digest
+files on every `watch` (local files you can serve or feed into any reader; nothing is emailed).
+
+## Quickstart
+```bash
+python3 -m venv .venv && .venv/bin/pip install -e '.[mcp]'     # PyPI package: not yet published
+source .venv/bin/activate
+
+bcf trials search --sponsor "Viking Therapeutics" --phase PHASE3
+bcf papers search --drug resmetirom --since 2026-09-01 --exclude mice rat --rank
+bcf grants search --pi "Ioannou, George N" --since 2024-01-01 --no-future
+bcf sec pdufa MDGL --since 2023-01-01
+bcf profile Lilly MDGL "Viking Therapeutics" --md profiles.md
+
+# watches: first run = baseline, later runs report what changed (cron it daily)
+bcf trials --db bcf.db watch --name obesity --condition obesity --phase PHASE3 --rss obesity.rss
+bcf papers --db bcf.db watch --name mdgl --affiliation "Madrigal Pharmaceuticals" --json-feed mdgl.feed.json
+```
+The old commands (`trialwatch`, `fdawatch`, `grantwatch`, `paperwatch`, `secwatch`, `trialwatch-mcp`) still work.
+
+### MCP server
+```json
+{"mcpServers": {"biocatalystfeed": {"command": "/path/to/.venv/bin/biocatalystfeed-mcp",
+  "env": {"BIOCATALYSTFEED_DB": "/path/to/bcf.db"}}}}
+```
+Tools include `search_trials`, `sponsor_pipeline`, `fda_approvals`, `company_profile`, `search_grants`,
+`search_papers`, `sec_pdufa_mentions`, `snapshot_*` / `*_changes_since`, and `changes_feed` (RSS / JSON Feed).
+
+### Configuration
+| Env var | Purpose |
+|---|---|
+| `BIOCATALYSTFEED_CONTACT` | contact email put in the SEC User-Agent (SEC fair-access policy). Default is a placeholder (`contact@biocatalystfeed.invalid`); **set it to your own contact before heavy SEC use** |
+| `SEC_USER_AGENT` | full SEC User-Agent override |
+| `NCBI_EMAIL` | optional email sent to NCBI E-utilities |
+| `BIOCATALYSTFEED_DB` (or `TRIALWATCH_DB`) | SQLite DB for the MCP server |
+| `FDAWATCH_ALIASES` | JSON file extending the company alias table |
+
+## How it compares
+Facts about DataLookout are from datalookout.com/citeline-alternative (checked 2026-10-12 PT). We have not tested
+their product.
+
+| | BioCatalystFeed (open source) | DataLookout |
+|---|---|---|
+| Price | Free (Apache-2.0); hosted tier planned | Free tier; Pro $49/month |
+| Sources | ClinicalTrials.gov, openFDA, NIH RePORTER, PubMed, Europe PMC, bioRxiv/medRxiv, SEC EDGAR | ClinicalTrials.gov |
+| Change tracking | Diffs between your own runs (trials: status, phase, enrollment, dates, sponsor, title, why stopped, results; plus FDA, grant, paper and SEC changes) | Daily scan; 13 fields incl. status, enrollment, primary endpoints, interventions, results, site counts, completion dates; changes marked Stopped/Notable/Minor |
+| Delivery | CLI, MCP server for AI agents, RSS/JSON Feed files, Apify actor | Morning email digest + dashboard inbox |
+| Watch limits | None when self-hosted | Free: 1 sponsor + 1 disease watchlist + 1 saved search; Pro: 10 of each |
+| Scheduling | You run it (cron, Apify schedule) | Hosted, daily |
+| Setup | Python install | "2 minutes" (their claim) |
+
+Pick DataLookout for a hosted, emailed, ClinicalTrials.gov-only digest. Pick BioCatalystFeed if you want several
+sources per company or ticker, agent/MCP access, or to self-host.
+
+## Data sources, limits and etiquette
+Built-in throttles follow each source's published policy (e.g. NIH RePORTER 1 req/s, NCBI ≤3 req/s without key, SEC
+≤10 req/s with a declared User-Agent, openFDA 1,000 req/day per IP without key). We store **metadata and links only**
+for papers/preprints, never abstracts. Change detection only covers your own runs; there's no historical backfill.
+PDUFA dates are regex extractions from 8-K text, not a calendar. Attributions are in [`NOTICE`](NOTICE). Design notes
+and per-source terms are in [`docs/DEVELOPER-NOTES.md`](docs/DEVELOPER-NOTES.md).
+
+## Hosted tier
+A paid hosted version (scheduled watches, persisted history, hosted MCP) is planned. Draft terms:
+[`TERMS.md`](TERMS.md), [`PRIVACY.md`](PRIVACY.md) (drafts, not legal advice, not in effect).
+
+## Contributing & licence
+See [`CONTRIBUTING.md`](CONTRIBUTING.md). Licensed under the [Apache License 2.0](LICENSE). BioCatalystFeed is
+independent and not endorsed by NLM, NIH, FDA, SEC, EMBL-EBI/Europe PMC, or bioRxiv/medRxiv.

biocatalystfeed-0.2.0/biocatalystfeed/__init__.py

@@ -0,0 +1,5 @@
+"""BioCatalystFeed: open-source monitors for biotech catalysts across ClinicalTrials.gov, openFDA, NIH RePORTER,
+PubMed / Europe PMC / bioRxiv / medRxiv and SEC EDGAR. Not investment, legal or medical advice."""
+__version__ = "0.2.0"
+DISCLAIMER = ("Not investment, legal or medical advice. Data may be incomplete, delayed or wrong; "
+              "PDUFA dates are unverified candidates from SEC filings.")

biocatalystfeed-0.2.0/biocatalystfeed/cli.py

@@ -0,0 +1,43 @@
+"""`biocatalystfeed` / `bcf` umbrella CLI: dispatches to the per-source tools (old commands still work as aliases)."""
+from __future__ import annotations
+import importlib, sys
+from . import __version__, DISCLAIMER
+
+TOOLS = {"trials": "trialwatch.cli", "fda": "fdawatch.cli", "grants": "grantwatch.cli", "papers": "paperwatch.cli",
+         "sec": "secwatch.cli", "mcp": "trialwatch.mcp_server"}
+ALIASES = {"trialwatch": "trials", "fdawatch": "fda", "grantwatch": "grants", "paperwatch": "papers", "secwatch": "sec",
+           "profile": "fda"}
+
+USAGE = f"""BioCatalystFeed {__version__}
+usage: biocatalystfeed <tool> [args...]     (short: bcf)
+
+tools:
+  trials   ClinicalTrials.gov search / watch / pipeline      (= trialwatch)
+  fda      openFDA approvals, labels, company profiles       (= fdawatch)
+  grants   NIH RePORTER grants                               (= grantwatch)
+  papers   PubMed + Europe PMC + bioRxiv/medRxiv             (= paperwatch)
+  sec      SEC EDGAR 8-K PDUFA mentions (UNVERIFIED)         (= secwatch)
+  profile  merged company profile                            (= fdawatch profile)
+  mcp      run the MCP server over stdio                     (= trialwatch-mcp)
+
+{DISCLAIMER}"""
+
+
+def main(argv=None):
+    argv = list(sys.argv[1:] if argv is None else argv)
+    if not argv or argv[0] in ("-h", "--help", "help"):
+        print(USAGE); return 0
+    if argv[0] in ("-V", "--version"):
+        print(__version__); return 0
+    tool = ALIASES.get(argv[0], argv[0])
+    if tool not in TOOLS:
+        print(f"unknown tool {argv[0]!r}\n\n{USAGE}", file=sys.stderr); return 2
+    rest = argv[1:]
+    if argv[0] == "profile": rest = ["profile"] + rest
+    mod = importlib.import_module(TOOLS[tool])
+    if tool == "mcp": return mod.main()
+    return mod.main(rest)
+
+
+if __name__ == "__main__":
+    sys.exit(main())

biocatalystfeed-0.2.0/biocatalystfeed.egg-info/PKG-INFO

@@ -0,0 +1,107 @@
+Metadata-Version: 2.4
+Name: biocatalystfeed
+Version: 0.2.0
+Summary: Open-source monitors for biotech catalysts: ClinicalTrials.gov, openFDA, NIH RePORTER, PubMed/Europe PMC/bioRxiv, SEC EDGAR. CLI + MCP server.
+License-Expression: Apache-2.0
+Keywords: biotech,clinical-trials,fda,pubmed,mcp,sec-edgar,monitoring
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: requests>=2.28
+Provides-Extra: mcp
+Requires-Dist: mcp>=1.2; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Dynamic: license-file
+
+# BioCatalystFeed
+
+**An open-source catalyst feed for biotech: see what changed across clinical trials, FDA actions, NIH grants,
+papers/preprints and SEC filings for the companies and drugs you follow.** Use it as a CLI, as an MCP server for AI
+agents (Claude, Cursor, …), or as an Apify actor.
+
+> ⚠️ **Not investment, legal or medical advice.** Data may be incomplete, delayed or wrong; PDUFA dates are unverified
+> candidates from SEC filings. Always check the linked primary source.
+
+## What it does
+| Source | Command | What you get |
+|---|---|---|
+| ClinicalTrials.gov API v2 (NLM) | `bcf trials` | search, sponsor pipelines, **diffs**: new trials, status/phase/enrollment/date changes |
+| openFDA (Drugs@FDA, SPL labels) | `bcf fda` | approvals (incl. novel NME/BLA flag), submissions, label revisions, diffs |
+| NIH RePORTER | `bcf grants` | grants by org / PI (middle-initial aware) / keyword; new awards, amount changes |
+| PubMed + **Europe PMC** + bioRxiv/medRxiv | `bcf papers` | papers & preprints, **deduplicated by DOI/PMID** across sources |
+| SEC EDGAR | `bcf sec` | 8-K mentions of PDUFA dates (UNVERIFIED candidates, linked to the filing) |
+| All of the above | `bcf profile` | one merged company profile (name or ticker) |
+
+Across tools: `--exclude TERM …` to drop noise, `--rank` for relevance ordering, and `--rss` / `--json-feed` digest
+files on every `watch` (local files you can serve or feed into any reader; nothing is emailed).
+
+## Quickstart
+```bash
+python3 -m venv .venv && .venv/bin/pip install -e '.[mcp]'     # PyPI package: not yet published
+source .venv/bin/activate
+
+bcf trials search --sponsor "Viking Therapeutics" --phase PHASE3
+bcf papers search --drug resmetirom --since 2026-09-01 --exclude mice rat --rank
+bcf grants search --pi "Ioannou, George N" --since 2024-01-01 --no-future
+bcf sec pdufa MDGL --since 2023-01-01
+bcf profile Lilly MDGL "Viking Therapeutics" --md profiles.md
+
+# watches: first run = baseline, later runs report what changed (cron it daily)
+bcf trials --db bcf.db watch --name obesity --condition obesity --phase PHASE3 --rss obesity.rss
+bcf papers --db bcf.db watch --name mdgl --affiliation "Madrigal Pharmaceuticals" --json-feed mdgl.feed.json
+```
+The old commands (`trialwatch`, `fdawatch`, `grantwatch`, `paperwatch`, `secwatch`, `trialwatch-mcp`) still work.
+
+### MCP server
+```json
+{"mcpServers": {"biocatalystfeed": {"command": "/path/to/.venv/bin/biocatalystfeed-mcp",
+  "env": {"BIOCATALYSTFEED_DB": "/path/to/bcf.db"}}}}
+```
+Tools include `search_trials`, `sponsor_pipeline`, `fda_approvals`, `company_profile`, `search_grants`,
+`search_papers`, `sec_pdufa_mentions`, `snapshot_*` / `*_changes_since`, and `changes_feed` (RSS / JSON Feed).
+
+### Configuration
+| Env var | Purpose |
+|---|---|
+| `BIOCATALYSTFEED_CONTACT` | contact email put in the SEC User-Agent (SEC fair-access policy). Default is a placeholder (`contact@biocatalystfeed.invalid`); **set it to your own contact before heavy SEC use** |
+| `SEC_USER_AGENT` | full SEC User-Agent override |
+| `NCBI_EMAIL` | optional email sent to NCBI E-utilities |
+| `BIOCATALYSTFEED_DB` (or `TRIALWATCH_DB`) | SQLite DB for the MCP server |
+| `FDAWATCH_ALIASES` | JSON file extending the company alias table |
+
+## How it compares
+Facts about DataLookout are from datalookout.com/citeline-alternative (checked 2026-10-12 PT). We have not tested
+their product.
+
+| | BioCatalystFeed (open source) | DataLookout |
+|---|---|---|
+| Price | Free (Apache-2.0); hosted tier planned | Free tier; Pro $49/month |
+| Sources | ClinicalTrials.gov, openFDA, NIH RePORTER, PubMed, Europe PMC, bioRxiv/medRxiv, SEC EDGAR | ClinicalTrials.gov |
+| Change tracking | Diffs between your own runs (trials: status, phase, enrollment, dates, sponsor, title, why stopped, results; plus FDA, grant, paper and SEC changes) | Daily scan; 13 fields incl. status, enrollment, primary endpoints, interventions, results, site counts, completion dates; changes marked Stopped/Notable/Minor |
+| Delivery | CLI, MCP server for AI agents, RSS/JSON Feed files, Apify actor | Morning email digest + dashboard inbox |
+| Watch limits | None when self-hosted | Free: 1 sponsor + 1 disease watchlist + 1 saved search; Pro: 10 of each |
+| Scheduling | You run it (cron, Apify schedule) | Hosted, daily |
+| Setup | Python install | "2 minutes" (their claim) |
+
+Pick DataLookout for a hosted, emailed, ClinicalTrials.gov-only digest. Pick BioCatalystFeed if you want several
+sources per company or ticker, agent/MCP access, or to self-host.
+
+## Data sources, limits and etiquette
+Built-in throttles follow each source's published policy (e.g. NIH RePORTER 1 req/s, NCBI ≤3 req/s without key, SEC
+≤10 req/s with a declared User-Agent, openFDA 1,000 req/day per IP without key). We store **metadata and links only**
+for papers/preprints, never abstracts. Change detection only covers your own runs; there's no historical backfill.
+PDUFA dates are regex extractions from 8-K text, not a calendar. Attributions are in [`NOTICE`](NOTICE). Design notes
+and per-source terms are in [`docs/DEVELOPER-NOTES.md`](docs/DEVELOPER-NOTES.md).
+
+## Hosted tier
+A paid hosted version (scheduled watches, persisted history, hosted MCP) is planned. Draft terms:
+[`TERMS.md`](TERMS.md), [`PRIVACY.md`](PRIVACY.md) (drafts, not legal advice, not in effect).
+
+## Contributing & licence
+See [`CONTRIBUTING.md`](CONTRIBUTING.md). Licensed under the [Apache License 2.0](LICENSE). BioCatalystFeed is
+independent and not endorsed by NLM, NIH, FDA, SEC, EMBL-EBI/Europe PMC, or bioRxiv/medRxiv.

biocatalystfeed-0.2.0/biocatalystfeed.egg-info/SOURCES.txt

@@ -0,0 +1,47 @@
+LICENSE
+NOTICE
+README.md
+pyproject.toml
+biocatalystfeed/__init__.py
+biocatalystfeed/cli.py
+biocatalystfeed.egg-info/PKG-INFO
+biocatalystfeed.egg-info/SOURCES.txt
+biocatalystfeed.egg-info/dependency_links.txt
+biocatalystfeed.egg-info/entry_points.txt
+biocatalystfeed.egg-info/requires.txt
+biocatalystfeed.egg-info/top_level.txt
+biowatch/__init__.py
+biowatch/digest.py
+biowatch/filters.py
+biowatch/http.py
+biowatch/store.py
+fdawatch/__init__.py
+fdawatch/aliases.py
+fdawatch/cli.py
+fdawatch/client.py
+fdawatch/core.py
+fdawatch/normalize.py
+fdawatch/report.py
+fdawatch/store.py
+grantwatch/__init__.py
+grantwatch/cli.py
+grantwatch/core.py
+paperwatch/__init__.py
+paperwatch/cli.py
+paperwatch/core.py
+secwatch/__init__.py
+secwatch/cli.py
+secwatch/core.py
+tests/test_biowatch.py
+tests/test_fdawatch.py
+tests/test_launch.py
+tests/test_mcp_stdio.py
+tests/test_trialwatch.py
+trialwatch/__init__.py
+trialwatch/cli.py
+trialwatch/client.py
+trialwatch/core.py
+trialwatch/mcp_server.py
+trialwatch/normalize.py
+trialwatch/report.py
+trialwatch/store.py

biocatalystfeed-0.2.0/biocatalystfeed.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

biocatalystfeed-0.2.0/biocatalystfeed.egg-info/entry_points.txt

@@ -0,0 +1,10 @@
+[console_scripts]
+bcf = biocatalystfeed.cli:main
+biocatalystfeed = biocatalystfeed.cli:main
+biocatalystfeed-mcp = trialwatch.mcp_server:main
+fdawatch = fdawatch.cli:main
+grantwatch = grantwatch.cli:main
+paperwatch = paperwatch.cli:main
+secwatch = secwatch.cli:main
+trialwatch = trialwatch.cli:main
+trialwatch-mcp = trialwatch.mcp_server:main

biocatalystfeed-0.2.0/biocatalystfeed.egg-info/requires.txt

@@ -0,0 +1,7 @@
+requests>=2.28
+
+[dev]
+pytest
+
+[mcp]
+mcp>=1.2