claudecode-omc 5.6.5 → 5.6.7

package/bundled/upstream/ecc/skills/scientific-db-uspto-database/SKILL.md

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+---
+name: uspto-database
+description: USPTO patent and trademark data workflow for official record lookup, PatentSearch queries, TSDR checks, assignment data, and reproducible IP research logs.
+origin: community
+---
+
+# USPTO Database
+
+Use this skill when a task needs official United States patent or trademark
+records from USPTO systems.
+
+## When to Use
+
+- Searching granted patents or pre-grant publications.
+- Checking patent application status, file-wrapper data, assignments, or
+  public prosecution history.
+- Looking up trademark status, documents, or assignment history.
+- Building reproducible prior-art, portfolio, or IP landscape research logs.
+- Comparing USPTO records with secondary tools such as Google Patents,
+  Lens.org, Semantic Scholar, or company patent pages.
+
+Do not use this skill to give legal advice. Treat it as a data-gathering and
+record-verification workflow.
+
+## Source Selection
+
+Prefer official USPTO or USPTO-supported surfaces first:
+
+- Open Data Portal (ODP): current home for migrated USPTO datasets and APIs.
+- Patent File Wrapper: public patent application bibliographic data and file
+  wrapper records.
+- PatentSearch API: PatentsView search API for granted patents and pre-grant
+  publication datasets.
+- TSDR Data API: trademark status and document retrieval.
+- Patent and Trademark Assignment Search: ownership transfer records.
+- PTAB data in ODP: Patent Trial and Appeal Board proceedings.
+
+Use secondary sources only as convenience indexes. When the answer matters,
+cross-check the official record.
+
+## Authentication and Secrets
+
+Many USPTO API flows require an API key. Store keys in environment variables or
+a secret manager, never in committed files or pasted transcripts.
+
+Common environment names:
+
+```bash
+export USPTO_API_KEY="..."
+export PATENTSVIEW_API_KEY="..."
+```
+
+For PatentSearch, send the key with the `X-Api-Key` header. For TSDR, follow
+the current USPTO API Manager instructions and rate-limit guidance.
+
+## PatentSearch Workflow
+
+Use PatentSearch for broad patent and pre-grant publication search when the
+question is about trends, inventors, assignees, classifications, dates, or
+portfolio slices.
+
+Workflow:
+
+1. Identify the endpoint from the current PatentSearch reference or Swagger UI.
+2. Build a JSON query with explicit filters.
+3. Request only the fields needed for the analysis.
+4. Sort and paginate deterministically.
+5. Record the endpoint, query body, date, data currency note, and result count.
+
+Python request skeleton:
+
+```python
+import os
+import requests
+
+API_KEY = os.environ["PATENTSVIEW_API_KEY"]
+BASE = "https://search.patentsview.org/api/v1"
+
+payload = {
+    "q": {
+        "_and": [
+            {"patent_date": {"_gte": "2024-01-01"}},
+            {"assignees.assignee_organization": {"_text_any": ["Google", "Alphabet"]}},
+        ]
+    },
+    "f": ["patent_id", "patent_title", "patent_date"],
+    "s": [{"patent_date": "desc"}],
+    "o": {"per_page": 100, "page": 1},
+}
+
+response = requests.post(
+    f"{BASE}/patent/",
+    headers={"X-Api-Key": API_KEY, "Content-Type": "application/json"},
+    json=payload,
+    timeout=30,
+)
+response.raise_for_status()
+print(response.json())
+```
+
+Before reusing a query, verify current endpoint names, field paths, request
+parameters, and API-key availability in the live PatentSearch docs.
+
+## Trademark/TSDR Workflow
+
+Use TSDR when the task needs trademark case status, documents, images, owner
+history, or prosecution events.
+
+Workflow:
+
+1. Normalize the serial number or registration number.
+2. Check the current TSDR API instructions and required API-key header.
+3. Fetch status first, then documents only if needed.
+4. Respect the lower rate limit for PDF, ZIP, and multi-case downloads.
+5. Capture retrieval date and serial/registration identifier in the output.
+
+For large trademark pulls, prefer documented bulk-data flows rather than
+screen-scraping public pages.
+
+## File Wrapper and Prosecution History
+
+For application status, transaction history, and prosecution documents:
+
+- Start with ODP Patent File Wrapper search.
+- Use exact identifiers when available: application number, publication number,
+  patent number, or party name.
+- Record whether the record is a granted patent, pre-grant publication, or
+  pending application.
+- Cross-check document dates and status against the record detail page before
+  citing them.
+
+## Assignment Workflow
+
+For patent or trademark ownership:
+
+1. Search official assignment data by patent/application/registration number,
+   assignor, assignee, or reel/frame when available.
+2. Record conveyance text, execution date, recordation date, and parties.
+3. Distinguish assignment records from current legal ownership conclusions.
+4. If ownership is material, flag the result for attorney or subject-matter
+   review.
+
+## Reproducible Output
+
+Every USPTO research pass should include a log table:
+
+```markdown
+| Source | Date searched | Identifier/query | Filters | Results | Notes |
+| --- | --- | --- | --- | ---: | --- |
+| PatentSearch | 2026-05-11 | `assignee=Alphabet AND date>=2024` | patent endpoint | 118 | API docs checked before run |
+| TSDR | 2026-05-11 | `serial=90000000` | status only | 1 | API-key flow, no document bulk pull |
+```
+
+For final writeups, separate:
+
+- official record facts
+- inferred analysis
+- secondary-source convenience matches
+- unresolved gaps or records that require legal review
+
+## Review Checklist
+
+- Did you use an official USPTO or USPTO-supported source first?
+- Did you verify current endpoint and field names before running code?
+- Are API keys kept out of files, shell history, and output logs?
+- Does the query log include the date searched and exact request shape?
+- Are rate limits respected?
+- Are legal conclusions avoided or explicitly escalated?
+- Are secondary sources labeled as secondary?
+
+## References
+
+- [USPTO APIs catalog](https://developer.uspto.gov/api-catalog)
+- [USPTO Open Data Portal](https://data.uspto.gov/)
+- [PatentSearch API reference](https://search.patentsview.org/docs/docs/Search%20API/SearchAPIReference/)
+- [PatentSearch API updates](https://search.patentsview.org/docs/)
+- [TSDR API bulk download FAQ](https://developer.uspto.gov/faq/tsdr-api-bulk-download)

package/bundled/upstream/ecc/skills/scientific-pkg-gget/SKILL.md

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+---
+name: gget
+description: gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
+origin: community
+---
+
+# gget
+
+Use this skill when a task needs quick bioinformatics lookup across genomic
+reference databases with the `gget` CLI or Python package.
+
+## When to Use
+
+- Finding Ensembl IDs, gene metadata, transcript details, or sequences.
+- Running quick BLAST or BLAT lookups without building a full local pipeline.
+- Fetching reference genome links and annotations from Ensembl.
+- Querying protein structure, pathway, cancer, expression, or disease-association
+  modules through a single interface.
+- Creating a reproducible first-pass evidence log before moving to heavier
+  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific
+  clients.
+
+Use a dedicated workflow instead of `gget` when the task requires regulated
+clinical interpretation, high-throughput production pipelines, or fine-grained
+control over database versions and local indexes.
+
+## Installation
+
+Use a clean Python environment.
+
+```bash
+python -m venv .venv
+. .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install --upgrade gget
+gget --help
+```
+
+If `uv` is available:
+
+```bash
+uv venv
+. .venv/bin/activate
+uv pip install gget
+```
+
+Before relying on an older environment, upgrade `gget` and re-check the module
+docs. The upstream databases queried by `gget` change over time.
+
+## Basic Patterns
+
+CLI shape:
+
+```bash
+gget <module> [arguments] [options]
+```
+
+Python shape:
+
+```python
+import gget
+
+result = gget.search(["BRCA1"], species="human")
+print(result)
+```
+
+Common workflow:
+
+1. Identify the species, assembly, gene ID type, and database needed.
+2. Check the current module documentation for arguments.
+3. Run a small query first.
+4. Save output with an explicit filename and date.
+5. Record module name, version, arguments, and database assumptions.
+
+## Common Modules
+
+Use current upstream docs for exact arguments. These modules are common first
+choices:
+
+- `gget search`: find Ensembl IDs from search terms.
+- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.
+- `gget seq`: fetch nucleotide or amino-acid sequences.
+- `gget ref`: retrieve reference genome download links.
+- `gget blast`: run a quick BLAST query.
+- `gget blat`: locate a sequence against supported genome assemblies.
+- `gget muscle`: run multiple sequence alignment.
+- `gget diamond`: run local sequence alignment against reference sequences.
+- `gget alphafold` and `gget pdb`: inspect protein-structure references.
+- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,
+  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease
+  association data.
+
+Do not assume every module supports every Python version or dependency set.
+Some optional scientific dependencies have narrower version support than the
+core package.
+
+## Quick Examples
+
+Find genes:
+
+```bash
+gget search -s human brca1 dna repair -o brca1-search.json
+```
+
+Fetch gene metadata:
+
+```bash
+gget info ENSG00000012048 -o brca1-info.json
+```
+
+Fetch a sequence:
+
+```bash
+gget seq ENSG00000012048 -o brca1-seq.fa
+```
+
+Run a small BLAST query:
+
+```bash
+gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json
+```
+
+Python example:
+
+```python
+import gget
+
+genes = gget.search(["BRCA1", "DNA repair"], species="human")
+info = gget.info(["ENSG00000012048"])
+sequence = gget.seq("ENSG00000012048")
+```
+
+## Reproducibility Log
+
+For scientific outputs, include enough metadata to replay the query.
+
+```markdown
+| Date | gget version | Module | Query | Species/assembly | Output | Notes |
+| --- | --- | --- | --- | --- | --- | --- |
+| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |
+```
+
+Also record:
+
+- Python version and environment manager.
+- Any optional dependency installed through `gget setup`.
+- Database-specific identifiers returned by the query.
+- Whether output is JSON, CSV, FASTA, or a DataFrame export.
+- Any failures that were resolved by upgrading `gget`.
+
+## Review Checklist
+
+- Did you upgrade or verify the installed `gget` version?
+- Did you check the current upstream module docs before using arguments?
+- Is the species or assembly explicit?
+- Are identifiers preserved exactly, including Ensembl/UniProt prefixes?
+- Is the result labeled as database output rather than clinical interpretation?
+- Is the query reproducible from the saved command or Python snippet?
+- Are optional dependencies installed in an isolated environment?
+
+## References
+
+- [gget documentation](https://pachterlab.github.io/gget/)
+- [gget updates](https://pachterlab.github.io/gget/en/updates.html)
+- [gget GitHub repository](https://github.com/pachterlab/gget)
+- [gget Bioinformatics paper](https://doi.org/10.1093/bioinformatics/btac836)

package/bundled/upstream/ecc/skills/scientific-thinking-literature-review/SKILL.md

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+---
+name: literature-review
+description: Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
+origin: community
+---
+
+# Literature Review
+
+Use this skill when the task is to find, screen, synthesize, and cite a body of
+academic or technical literature.
+
+## When to Use
+
+- Building a systematic, scoping, or narrative literature review.
+- Synthesizing the state of the art for a research question.
+- Finding gaps, contradictions, or future-work directions.
+- Preparing citation-backed background sections for papers or reports.
+- Comparing evidence across peer-reviewed papers, preprints, patents, and
+  technical reports.
+
+## Review Types
+
+- **Narrative review**: broad synthesis; useful for orientation.
+- **Scoping review**: maps concepts, methods, and evidence gaps.
+- **Systematic review**: predefined protocol, reproducible search, explicit
+  screening and exclusion.
+- **Meta-analysis**: systematic review plus quantitative effect aggregation.
+
+Ask the user which level of rigor is needed. If unspecified, default to a
+scoping review for exploratory work and a systematic review for publication or
+clinical claims.
+
+## Workflow
+
+### 1. Define the Question
+
+Convert the prompt into a searchable research question.
+
+For clinical or biomedical work, use PICO:
+
+- Population
+- Intervention or exposure
+- Comparator
+- Outcome
+
+For technical work, use:
+
+- system or domain
+- method or intervention
+- comparison baseline
+- evaluation metric
+
+### 2. Plan the Search
+
+Create a search protocol before collecting sources:
+
+- databases to search
+- date range
+- languages
+- publication types
+- inclusion criteria
+- exclusion criteria
+- exact search strings
+
+Minimum useful database set:
+
+- PubMed for biomedical and life-sciences literature.
+- arXiv for CS, math, physics, quantitative biology, and preprints.
+- Semantic Scholar or Crossref for broad academic discovery.
+- Domain-specific sources when relevant, such as clinical-trial registries,
+  patent databases, standards bodies, or official technical docs.
+
+### 3. Search and Log Evidence
+
+Keep a search log that makes the review reproducible:
+
+```markdown
+| Database | Date searched | Query | Filters | Results | Export |
+| --- | --- | --- | --- | ---: | --- |
+| PubMed | 2026-05-11 | `("CRISPR"[tiab] OR "Cas9"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |
+| arXiv | 2026-05-11 | `CRISPR sickle cell gene editing` | q-bio, 2020:2026 | 9 | BibTeX |
+```
+
+Save raw IDs, URLs, DOIs, abstracts, and notes separately from the final prose.
+
+### 4. Deduplicate
+
+Deduplicate in this order:
+
+1. DOI
+2. PMID or arXiv ID
+3. exact title
+4. normalized title plus first author and year
+
+Record how many duplicates were removed.
+
+### 5. Screen Sources
+
+Screen in stages:
+
+1. title
+2. abstract
+3. full text
+
+For systematic work, record exclusion reasons:
+
+- wrong population
+- wrong intervention
+- wrong outcome
+- not primary research
+- duplicate
+- unavailable full text
+- outside date range
+
+### 6. Extract Data
+
+Use a structured extraction table:
+
+```markdown
+| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| Author Year | RCT/cohort/review/etc. | sample or corpus | method | baseline | measured outcome | result | caveat |
+```
+
+For technical papers, include dataset, benchmark, metric, baseline, and
+reproducibility notes.
+
+### 7. Synthesize
+
+Group evidence by theme rather than summarizing papers one by one.
+
+Useful synthesis lenses:
+
+- strongest evidence
+- conflicting evidence
+- methodological weaknesses
+- population or dataset limits
+- recency and replication
+- practical implications
+- unanswered questions
+
+Separate claims by confidence:
+
+- **High confidence**: replicated, high-quality evidence across sources.
+- **Medium confidence**: plausible but limited by sample, method, or recency.
+- **Low confidence**: early, speculative, single-source, or weakly measured.
+
+### 8. Verify Citations
+
+Before finalizing:
+
+- verify DOI, PMID, arXiv ID, or official URL
+- check author names and publication year
+- do not cite a paper for a claim it does not make
+- mark preprints as preprints
+- distinguish reviews from primary evidence
+
+## Output Template
+
+```markdown
+# Literature Review: <Topic>
+
+Generated: <date>
+Review type: <narrative | scoping | systematic | meta-analysis>
+Search window: <dates>
+Databases: <list>
+
+## Research Question
+
+## Search Strategy
+
+## Inclusion and Exclusion Criteria
+
+## Evidence Summary
+
+## Thematic Synthesis
+
+## Gaps and Limitations
+
+## References
+
+## Search Log
+```
+
+## Pitfalls
+
+- Do not treat search snippets as evidence.
+- Do not mix preprints, reviews, and primary studies without labeling them.
+- Do not omit negative or conflicting findings.
+- Do not claim systematic-review rigor without a reproducible protocol.
+- Do not use a single database for a broad claim unless the scope is explicitly
+  limited to that database.

package/bundled/upstream/ecc/skills/scientific-thinking-scholar-evaluation/SKILL.md

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+---
+name: scholar-evaluation
+description: Structured scholarly-work evaluation for papers, proposals, literature reviews, methods sections, evidence quality, citation support, and research-writing feedback.
+origin: community
+---
+
+# Scholar Evaluation
+
+Use this skill to evaluate academic or scientific work with a repeatable rubric.
+
+## When to Use
+
+- Reviewing a research paper, proposal, thesis chapter, or literature review.
+- Checking whether claims are supported by cited evidence.
+- Evaluating methodology, study design, analysis, or limitations.
+- Comparing two or more papers for quality or relevance.
+- Producing structured feedback for revision.
+
+## Evaluation Scope
+
+Start by identifying the artifact:
+
+- empirical research paper
+- theoretical paper
+- technical report
+- systematic or narrative literature review
+- research proposal
+- thesis or dissertation chapter
+- conference abstract or short paper
+
+Then choose scope:
+
+- **comprehensive**: all rubric dimensions
+- **targeted**: one or two dimensions, such as method or citations
+- **comparative**: rank multiple works against the same rubric
+
+## Rubric
+
+Score each applicable dimension from 1 to 5:
+
+- 5: excellent; clear, rigorous, and publication-ready
+- 4: good; minor improvements needed
+- 3: adequate; meaningful gaps but usable
+- 2: weak; substantial revision needed
+- 1: poor; major validity or clarity problems
+
+Use `N/A` for dimensions that do not apply.
+
+### 1. Problem and Research Question
+
+- Is the problem clear and specific?
+- Is the contribution meaningful?
+- Are scope and assumptions explicit?
+- Does the question match the claimed contribution?
+
+### 2. Literature and Context
+
+- Is relevant prior work covered?
+- Does the work synthesize rather than merely list sources?
+- Are gaps accurately identified?
+- Are recent and foundational sources balanced?
+
+### 3. Methodology
+
+- Does the method answer the research question?
+- Are design choices justified?
+- Are variables, datasets, participants, or materials described clearly?
+- Could another researcher reproduce the work?
+- Are ethical and practical constraints acknowledged?
+
+### 4. Data and Evidence
+
+- Are data sources credible and appropriate?
+- Is sample size or corpus coverage adequate?
+- Are inclusion, exclusion, and preprocessing decisions documented?
+- Are missing data and bias risks discussed?
+
+### 5. Analysis
+
+- Are statistical, qualitative, or computational methods appropriate?
+- Are baselines and controls fair?
+- Are uncertainty, sensitivity, or robustness checks included when needed?
+- Are alternative explanations considered?
+
+### 6. Results and Interpretation
+
+- Are results clearly presented?
+- Do claims stay within the evidence?
+- Are figures, tables, and metrics understandable?
+- Are negative or null results handled honestly?
+
+### 7. Limitations and Threats to Validity
+
+- Are limitations specific rather than generic?
+- Are internal, external, construct, and conclusion-validity risks addressed?
+- Does the paper distinguish speculation from demonstrated results?
+
+### 8. Writing and Structure
+
+- Is the argument easy to follow?
+- Are sections organized around the research question?
+- Are definitions and notation clear?
+- Is the tone precise and scholarly?
+
+### 9. Citations
+
+- Do cited papers support the claims attached to them?
+- Are primary sources used where possible?
+- Are reviews labeled as reviews?
+- Are preprints labeled as preprints?
+- Are citation metadata and links correct?
+
+## Review Process
+
+1. Read the abstract, introduction, figures, and conclusion for claimed
+   contribution.
+2. Read methods and results for evidence quality.
+3. Check the strongest claims against cited sources.
+4. Score each applicable dimension.
+5. Separate critical blockers from revision suggestions.
+6. End with concrete next edits.
+
+## Output Template
+
+```markdown
+# Scholar Evaluation: <Artifact>
+
+## Overall Assessment
+
+- Overall score: <1-5 or N/A>
+- Confidence: <high | medium | low>
+- Summary: <3-5 sentences>
+
+## Dimension Scores
+
+| Dimension | Score | Evidence | Revision priority |
+| --- | ---: | --- | --- |
+| Problem and question |  |  |  |
+| Literature and context |  |  |  |
+| Methodology |  |  |  |
+| Data and evidence |  |  |  |
+| Analysis |  |  |  |
+| Results and interpretation |  |  |  |
+| Limitations |  |  |  |
+| Writing and structure |  |  |  |
+| Citations |  |  |  |
+
+## Critical Issues
+
+## Recommended Revisions
+
+## Evidence Checks Needed
+```
+
+## Pitfalls
+
+- Do not use the score as a substitute for concrete feedback.
+- Do not penalize a paper for omitting a dimension outside its scope.
+- Do not treat citation count, venue, or author reputation as proof of quality.
+- Do not accept unsupported claims just because they appear in the abstract.