omicsmeta 0.1.0__tar.gz

omicsmeta-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+name: CI
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install package and test dependencies
+        run: python -m pip install -e ".[dev]"
+
+      - name: Run tests
+        run: python -m pytest --cov=omicsmeta --cov-report=term-missing --cov-fail-under=70
+
+  package:
+    name: Package artifacts
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Build and check distributions
+        run: |
+          python -m pip install build twine
+          python -m build
+          python -m twine check dist/*.tar.gz dist/*.whl
+
+      - name: Install wheel and smoke-test CLI
+        run: |
+          python -m pip install dist/omicsmeta-*.whl
+          omicsmeta --help

omicsmeta-0.1.0/.github/workflows/pages.yml

@@ -0,0 +1,63 @@
+name: Docs
+
+on:
+  push:
+    branches: ["main"]
+    paths:
+      - ".github/workflows/pages.yml"
+      - "docs/**"
+      - "mkdocs.yml"
+      - "pyproject.toml"
+      - "README.md"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build MkDocs site
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install documentation dependencies
+        run: python -m pip install -e ".[docs]"
+
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v5
+
+      - name: Build documentation
+        run: mkdocs build --strict --site-dir site
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    name: Deploy GitHub Pages
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

omicsmeta-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,58 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published, released]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install build tools
+        run: python -m pip install build twine
+
+      - name: Build source and wheel distributions
+        run: python -m build
+
+      - name: Validate distributions
+        run: python -m twine check dist/*.tar.gz dist/*.whl
+
+      - name: Upload distribution artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    name: Publish distributions to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/omicsmeta/
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distribution artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

omicsmeta-0.1.0/.gitignore

@@ -0,0 +1,18 @@
+.DS_Store
+.env
+.env.*
+!.env.example
+.pytest_cache/
+.ruff_cache/
+.tmp/
+.coverage
+htmlcov/
+site/
+dist/
+build/
+*.egg-info/
+__pycache__/
+*.py[cod]
+.venv/
+venv/
+to-do.md

omicsmeta-0.1.0/CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+All notable changes to `omicsmeta` will be documented in this file.
+
+The project is currently pre-alpha.
+
+## 0.1.0 - 2026-06-13
+
+- Added a Python package scaffold with CLI entry point.
+- Added normalization, field detection, mapping, validation, and harmonization
+  modules.
+- Added tabular, minimal GEO SOFT, BioSample XML, and SRA XML readers.
+- Added detailed harmonized, unmapped, unmapped-summary, sample-wide, and HTML
+  QC outputs.
+- Added managed ontology resource download and SQLite indexing commands.
+- Added conservative handling for ambiguous metadata fields.
+- Added transparent cell-line inference for common cell lines.
+- Added batch harmonization for multiple files and GEO accessions.
+- Added known-answer benchmark helper and CLI script.
+- Added a multi-fixture known-answer benchmark suite.
+- Added integration fixtures based on GEO-style metadata snippets.
+- Added public documentation, contribution metadata, and a JOSS paper skeleton.
+- Added a Galaxy wrapper scaffold with local wrapper smoke test data.
+- Added package artifact build validation and a release-readiness checklist.
+- Added SRA/BioSample XML edge-case coverage for namespaced documents,
+  repeated attributes, and accession fallbacks.
+- Added GitHub Pages documentation publishing and a Material for MkDocs site
+  theme.

omicsmeta-0.1.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,31 @@
+# Code of Conduct
+
+`omicsmeta` aims to be a respectful, practical, and technically rigorous open
+source project.
+
+## Expected Behavior
+
+- Treat contributors and users with respect.
+- Discuss technical disagreements with evidence and clear reasoning.
+- Keep feedback specific to the code, documentation, data, or scientific claim.
+- Assume public project spaces are read by people who do not know the private
+  context behind a discussion.
+
+## Unacceptable Behavior
+
+- Harassment, discrimination, intimidation, or personal attacks.
+- Publishing private information without explicit permission.
+- Repeated disruption of project discussions after maintainers ask for a change
+  in behavior.
+- Knowingly submitting fabricated data, misleading benchmark results, or
+  unsupported scientific claims.
+
+## Enforcement
+
+Maintainers may remove comments, close issues, reject contributions, or restrict
+participation when behavior conflicts with this code of conduct. Enforcement
+decisions should be documented privately among maintainers with enough context
+to review them later.
+
+Report conduct concerns to the current project maintainers through the issue
+tracker or another maintainer-provided contact channel.

omicsmeta-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,55 @@
+# Contributing
+
+Thank you for considering a contribution to `omicsmeta`. The project is
+pre-alpha, so the highest-value contributions are focused tests, small bug
+fixes, documentation improvements, and real metadata examples with expected
+outputs.
+
+## Development Setup
+
+```bash
+python -m pip install -e ".[dev]"
+python -m pytest
+```
+
+Run the coverage gate used during development:
+
+```bash
+python -m pytest --cov=omicsmeta --cov-report=term-missing --cov-fail-under=70
+```
+
+## Contribution Guidelines
+
+- Keep changes focused. A pull request should usually address one feature,
+  bug, fixture, or documentation topic.
+- Add tests for new behavior, especially field detection, ontology mapping,
+  validation, CLI output, and real metadata fixtures.
+- Preserve provenance in outputs. New transformations should keep enough source
+  context for a curator to audit the result.
+- Prefer conservative defaults. Uncertain mappings should be reported for
+  review instead of silently accepted.
+- Public documentation should assume readers do not know any prior discussion
+  about the project.
+
+## Reporting Issues
+
+Useful issue reports include:
+
+- the exact command or Python snippet that failed;
+- a small input file or fixture;
+- expected and actual outputs;
+- the installed `omicsmeta` version or commit hash;
+- whether the issue involves local OBO files, managed ontology resources, or
+  the optional `text2term` backend.
+
+## Release Readiness
+
+Before any release intended for external users, maintainers should verify that
+the test suite passes, documentation examples run from a clean checkout, and the
+paper and citation metadata do not overstate the validation status of the
+software.
+
+See the public [release readiness checklist](docs/release_readiness.md) for the
+artifact build, documentation, benchmark, and manual review checks. The
+checklist validates readiness only; publishing requires explicit maintainer
+approval.

omicsmeta-0.1.0/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2026 omicsmeta contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

omicsmeta-0.1.0/PKG-INFO

@@ -0,0 +1,167 @@
+Metadata-Version: 2.4
+Name: omicsmeta
+Version: 0.1.0
+Summary: Automated harmonization of public omics metadata
+Project-URL: Homepage, https://github.com/qchiujunhao/omicsmeta
+Project-URL: Documentation, https://qchiujunhao.github.io/omicsmeta/
+Project-URL: Issues, https://github.com/qchiujunhao/omicsmeta/issues
+Author: omicsmeta contributors
+License-Expression: MIT
+License-File: LICENSE
+Keywords: BioSample,GEO,SRA,bioinformatics,metadata,ontology
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: pandas>=2.0
+Requires-Dist: requests>=2.31
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=5; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocs<2,>=1.6; extra == 'docs'
+Provides-Extra: fuzzy
+Requires-Dist: rapidfuzz>=3.0; extra == 'fuzzy'
+Provides-Extra: ontology
+Requires-Dist: pronto>=2.5; extra == 'ontology'
+Provides-Extra: text2term
+Requires-Dist: text2term; extra == 'text2term'
+Description-Content-Type: text/markdown
+
+# omicsmeta
+
+`omicsmeta` is an early-stage Python package for harmonizing public omics
+metadata from GEO, SRA, BioSample, and tabular exports.
+
+The central design choice is to make ontology mapping pluggable. Generic
+mapping tools such as `text2term` are useful, but public omics metadata also
+needs domain-specific preprocessing, field-type detection, confidence-aware
+routing, and cross-field validation. `omicsmeta` is intended to provide that
+pipeline.
+
+Current implementation status:
+
+- string normalization and biomedical abbreviation expansion
+- heuristic metadata field detection
+- lightweight built-in ontology mapper for common terms
+- optional `text2term` mapper adapter
+- simple OBO loader and SQLite ontology cache
+- tabular, minimal GEO SOFT, BioSample XML, and SRA XML readers
+- harmonization orchestrator and CLI
+- real GEO SOFT snippet test coverage
+- conservative field routing for ambiguous metadata columns
+- transparent cell-line inference for missing species/tissue/disease fields
+- deduplicated unmapped-term summaries for manual curation
+- sample-wide output tables
+- batch harmonization
+- known-answer benchmark helper and CLI script
+
+Example:
+
+```bash
+omicsmeta harmonize metadata.tsv \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Direct GEO fetching is also available:
+
+```bash
+omicsmeta harmonize \
+  --geo-accession GSE123456 \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Custom local OBO files can be added to the built-in mapper:
+
+```bash
+omicsmeta harmonize metadata.tsv \
+  --ontology-obo disease_slim.obo \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Managed ontology resources can be cached locally:
+
+```bash
+omicsmeta ontologies list
+omicsmeta ontologies download doid uberon cl
+omicsmeta ontologies index --resource doid --resource uberon
+omicsmeta harmonize metadata.tsv \
+  --ontology-resource doid \
+  --ontology-resource uberon \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Multiple files can be harmonized in one run:
+
+```bash
+omicsmeta batch \
+  --input metadata_a.tsv \
+  --input metadata_b.tsv \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Known-answer fixtures can be benchmarked:
+
+```bash
+python scripts/benchmark_mapping.py \
+  --input examples/basic/metadata.tsv \
+  --truth examples/basic/expected_harmonized.tsv
+```
+
+Run the bundled multi-fixture benchmark suite:
+
+```bash
+python scripts/benchmark_mapping.py \
+  --manifest benchmarks/known_answer_suite.tsv \
+  --output-json benchmark_suite.json
+```
+
+## Documentation
+
+- [Documentation site](https://qchiujunhao.github.io/omicsmeta/)
+- [Quickstart](docs/quickstart.md)
+- [API reference](docs/api.md)
+- [Design notes](docs/design.md)
+- [Release readiness checklist](docs/release_readiness.md)
+- [Basic fixture tutorial](docs/tutorials/basic_fixture.md)
+- [Galaxy wrapper scaffold](galaxy-omicsmeta/omicsmeta_harmonize.xml)
+
+## Maturity
+
+This repository is pre-alpha and not yet JOSS-ready. The implemented code is
+tested, but the project still needs publication-scale curated benchmarks,
+release packaging, external user feedback, and Galaxy Tool Shed validation
+before submission.
+
+Run tests locally with:
+
+```bash
+python -m pip install -e ".[dev]"
+python -m pytest
+```

omicsmeta-0.1.0/README.md

@@ -0,0 +1,131 @@
+# omicsmeta
+
+`omicsmeta` is an early-stage Python package for harmonizing public omics
+metadata from GEO, SRA, BioSample, and tabular exports.
+
+The central design choice is to make ontology mapping pluggable. Generic
+mapping tools such as `text2term` are useful, but public omics metadata also
+needs domain-specific preprocessing, field-type detection, confidence-aware
+routing, and cross-field validation. `omicsmeta` is intended to provide that
+pipeline.
+
+Current implementation status:
+
+- string normalization and biomedical abbreviation expansion
+- heuristic metadata field detection
+- lightweight built-in ontology mapper for common terms
+- optional `text2term` mapper adapter
+- simple OBO loader and SQLite ontology cache
+- tabular, minimal GEO SOFT, BioSample XML, and SRA XML readers
+- harmonization orchestrator and CLI
+- real GEO SOFT snippet test coverage
+- conservative field routing for ambiguous metadata columns
+- transparent cell-line inference for missing species/tissue/disease fields
+- deduplicated unmapped-term summaries for manual curation
+- sample-wide output tables
+- batch harmonization
+- known-answer benchmark helper and CLI script
+
+Example:
+
+```bash
+omicsmeta harmonize metadata.tsv \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Direct GEO fetching is also available:
+
+```bash
+omicsmeta harmonize \
+  --geo-accession GSE123456 \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Custom local OBO files can be added to the built-in mapper:
+
+```bash
+omicsmeta harmonize metadata.tsv \
+  --ontology-obo disease_slim.obo \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Managed ontology resources can be cached locally:
+
+```bash
+omicsmeta ontologies list
+omicsmeta ontologies download doid uberon cl
+omicsmeta ontologies index --resource doid --resource uberon
+omicsmeta harmonize metadata.tsv \
+  --ontology-resource doid \
+  --ontology-resource uberon \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Multiple files can be harmonized in one run:
+
+```bash
+omicsmeta batch \
+  --input metadata_a.tsv \
+  --input metadata_b.tsv \
+  --output harmonized.tsv \
+  --unmapped unmapped.tsv \
+  --unmapped-summary-output unmapped_summary.tsv \
+  --sample-output samples.tsv \
+  --report qc_report.html
+```
+
+Known-answer fixtures can be benchmarked:
+
+```bash
+python scripts/benchmark_mapping.py \
+  --input examples/basic/metadata.tsv \
+  --truth examples/basic/expected_harmonized.tsv
+```
+
+Run the bundled multi-fixture benchmark suite:
+
+```bash
+python scripts/benchmark_mapping.py \
+  --manifest benchmarks/known_answer_suite.tsv \
+  --output-json benchmark_suite.json
+```
+
+## Documentation
+
+- [Documentation site](https://qchiujunhao.github.io/omicsmeta/)
+- [Quickstart](docs/quickstart.md)
+- [API reference](docs/api.md)
+- [Design notes](docs/design.md)
+- [Release readiness checklist](docs/release_readiness.md)
+- [Basic fixture tutorial](docs/tutorials/basic_fixture.md)
+- [Galaxy wrapper scaffold](galaxy-omicsmeta/omicsmeta_harmonize.xml)
+
+## Maturity
+
+This repository is pre-alpha and not yet JOSS-ready. The implemented code is
+tested, but the project still needs publication-scale curated benchmarks,
+release packaging, external user feedback, and Galaxy Tool Shed validation
+before submission.
+
+Run tests locally with:
+
+```bash
+python -m pip install -e ".[dev]"
+python -m pytest
+```

omicsmeta-0.1.0/benchmarks/README.md

@@ -0,0 +1,25 @@
+# Benchmark Fixtures
+
+This directory contains a small known-answer benchmark suite for regression
+testing and development. It is not a publication-scale validation dataset.
+
+`known_answer_suite.tsv` is a manifest with one benchmark case per row:
+
+- `name`: stable case identifier.
+- `input_path`: metadata input path, relative to this directory unless absolute.
+- `input_type`: `tabular` or `geo_soft`.
+- `truth_path`: expected mapping table, relative to this directory unless
+  absolute.
+- `description`: short human-readable case description.
+
+Truth tables are stored in `truth/`. Each truth row is scored by
+`sample_id`, `field_type`, and `ontology_id`; extra columns such as `label` are
+for reader context.
+
+Run the suite from the repository root:
+
+```bash
+python scripts/benchmark_mapping.py \
+  --manifest benchmarks/known_answer_suite.tsv \
+  --output-json benchmark_suite.json
+```

omicsmeta-0.1.0/benchmarks/known_answer_suite.tsv

@@ -0,0 +1,9 @@
+name	input_path	input_type	truth_path	description
+basic_tabular	../examples/basic/metadata.tsv	tabular	truth/basic_expected_harmonized.tsv	Small tabular fixture with disease, tissue, species, sex, and cell-line fields.
+geo_lung_a549	../tests/fixtures/GSE154243_soft_snippet.txt	geo_soft	truth/GSE154243_expected_harmonized.tsv	GEO-style A549 lung adenocarcinoma metadata with a typo in source text.
+immune_pbmc	../tests/fixtures/immune_pbmc_soft_snippet.txt	geo_soft	truth/immune_pbmc_expected_harmonized.tsv	GEO-style immune blood metadata with sex and species fields.
+mouse_liver	../tests/fixtures/mouse_liver_soft_snippet.txt	geo_soft	truth/mouse_liver_expected_harmonized.tsv	GEO-style mouse liver metadata with organism, tissue, and sex fields.
+treatment_perturbation	../tests/fixtures/treatment_perturbation_soft_snippet.txt	geo_soft	truth/treatment_perturbation_expected_harmonized.tsv	GEO-style treatment metadata where perturbation terms remain review items.
+ambiguous_phenotype	../tests/fixtures/ambiguous_phenotype_soft_snippet.txt	geo_soft	truth/ambiguous_phenotype_expected_harmonized.tsv	GEO-style ambiguous phenotype metadata that should not force phenotype terms into disease.
+biosample_xml	../tests/fixtures/biosample_snippet.xml	biosample_xml	truth/biosample_expected_harmonized.tsv	BioSample XML fixture with attributes for disease, tissue, sex, species, and cell line.
+sra_xml	../tests/fixtures/sra_snippet.xml	sra_xml	truth/sra_expected_harmonized.tsv	SRA XML fixture with SAMPLE_ATTRIBUTE disease, tissue, species, and cell-line fields.

omicsmeta-0.1.0/benchmarks/truth/GSE154243_expected_harmonized.tsv

@@ -0,0 +1,9 @@
+sample_id	field_type	ontology_id	label
+GSM4667502	cell_line	CVCL:0023	A549
+GSM4667502	species	NCBITaxon:9606	Homo sapiens
+GSM4667502	tissue	UBERON:0002048	lung
+GSM4667502	disease	DOID:299	adenocarcinoma
+GSM4667503	species	NCBITaxon:9606	Homo sapiens
+GSM4667503	tissue	UBERON:0002048	lung
+GSM4667503	cell_line	CVCL:0023	A549
+GSM4667503	disease	DOID:299	adenocarcinoma

omicsmeta-0.1.0/benchmarks/truth/ambiguous_phenotype_expected_harmonized.tsv

@@ -0,0 +1,5 @@
+sample_id	field_type	ontology_id	label
+GSMAMB1	species	NCBITaxon:9606	Homo sapiens
+GSMAMB1	tissue	UBERON:0000310	breast
+GSMAMB2	species	NCBITaxon:9606	Homo sapiens
+GSMAMB2	tissue	UBERON:0000310	breast