diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 4d9998ba..b08ce399 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -1,116 +1,69 @@ name: Lint and Test on: - workflow_call: + workflow_call: -jobs: - run_unit_tests: - runs-on: ubuntu-latest - if: 1 == 0 - strategy: - fail-fast: false - - steps: - - name: Repo checkout - uses: actions/checkout@main - - - name: Set up Python 3. - uses: actions/setup-python@main - with: - python-version: 3.12 - - - name: Install uv - uses: astral-sh/setup-uv@v6 - - - name: Install dependencies - id: install_deps - run: uv sync - - - name: run pytest -rP tests/ - id: run_pytest - run: | - uv run pytest --cov=credit_engine --cov-report=xml -rP tests/ - continue-on-error: true - - - name: Send to Codecov - id: send_to_codecov - uses: codecov/codecov-action@main - continue-on-error: true - with: - files: ./coverage.xml - fail_ci_if_error: true - token: ${{ secrets.CODECOV_TOKEN }} - - - name: outcome failure - if: steps.run_pytest.outcome != 'success' || steps.send_to_codecov.outcome != 'success' - run: | - echo "Python tests: ${{ steps.run_pytest.outcome }}" - echo "upload coverage: ${{ steps.send_to_codecov.outcome }}" - exit 1 - - - name: outcome success - run: | - echo "Python tests: ${{ steps.run_pytest.outcome }}" - echo "upload coverage: ${{ steps.send_to_codecov.outcome }}" - exit 0 - - run_linkml_tasks: - runs-on: ubuntu-latest - strategy: - fail-fast: false +permissions: + contents: read - steps: - - name: Repo checkout - uses: actions/checkout@main - - - name: Set up Python 3. - uses: actions/setup-python@main - with: - python-version: 3.12 - - - name: Install uv - uses: astral-sh/setup-uv@v6 - - - name: Install dependencies - id: install_deps - run: uv sync - - - name: Lint linkml file - id: lint_linkml - run: | - make lint-no-warn - continue-on-error: true - - - name: Validate sample data against the schema - id: test_sample_data - run: | - make test-sample-data - continue-on-error: true - - - name: Validate sample data against JSONschema - id: test_sample_data_jsonschema - run: | - make test-sample-data-jsonschema - continue-on-error: true - - - name: Test documentation generation - id: test_docgen - run: | - uv sync --group docs - make gendoc - continue-on-error: true - - - name: outcome failure - if: steps.lint_linkml.outcome != 'success' || steps.test_sample_data.outcome != 'success' || steps.test_sample_data_jsonschema.outcome != 'success' || steps.test_docgen.outcome != 'success' - run: | - echo "linkml linting: ${{ steps.lint_linkml.outcome }}" - echo "sample data validation: ${{ steps.test_sample_data.outcome }}" - echo "sample data JSON Schema validation: ${{ steps.test_sample_data_jsonschema.outcome }}" - echo "documentation generator: ${{ steps.test_docgen.outcome }}" - exit 1 - - - name: outcome success - if: steps.lint_linkml.outcome == 'success' && steps.test_sample_data.outcome == 'success' && steps.test_sample_data_jsonschema.outcome == 'success' && steps.test_docgen.outcome == 'success' - run: | - echo All tests passed successfully! - exit 0 +jobs: + run_linkml_tasks: + runs-on: ubuntu-latest + strategy: + fail-fast: false + + steps: + - name: Repo checkout + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 + + - name: Setup python + uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 + with: + python-version: "3.14" + + - name: Install uv + uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e + with: + python-version: 3.14 + + - name: Install project + run: uv sync --frozen --group docs + + - name: Lint linkml file + id: lint_linkml + run: | + make lint-no-warn + continue-on-error: true + + - name: Validate sample data against the schema + id: test_sample_data + run: | + make test-sample-data + continue-on-error: true + + - name: Validate sample data against JSONschema + id: test_sample_data_jsonschema + run: | + make test-sample-data-jsonschema + continue-on-error: true + + - name: Test documentation generation + id: test_docgen + run: | + make gendoc + continue-on-error: true + + - name: outcome failure + if: steps.lint_linkml.outcome != 'success' || steps.test_sample_data.outcome != 'success' || steps.test_sample_data_jsonschema.outcome != 'success' || steps.test_docgen.outcome != 'success' + run: | + echo "linkml linting: ${{ steps.lint_linkml.outcome }}" + echo "sample data validation: ${{ steps.test_sample_data.outcome }}" + echo "sample data JSON Schema validation: ${{ steps.test_sample_data_jsonschema.outcome }}" + echo "documentation generator: ${{ steps.test_docgen.outcome }}" + exit 1 + + - name: outcome success + if: steps.lint_linkml.outcome == 'success' && steps.test_sample_data.outcome == 'success' && steps.test_sample_data_jsonschema.outcome == 'success' && steps.test_docgen.outcome == 'success' + run: | + echo All tests passed successfully! + exit 0 diff --git a/.github/workflows/update_kbase_dois.yaml b/.github/workflows/update_kbase_dois.yaml new file mode 100644 index 00000000..87ce4034 --- /dev/null +++ b/.github/workflows/update_kbase_dois.yaml @@ -0,0 +1,51 @@ +name: Update KBase DOI List + +on: + schedule: + # Runs weekly on Mondays at 08:00 UTC + - cron: "0 8 * * 1" + workflow_dispatch: + +permissions: + contents: write + pull-requests: write + +jobs: + update-kbase-dois: + runs-on: ubuntu-latest + name: Generate and update KBase DOI list + steps: + - name: Checkout repository + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 + with: + ref: main + + - name: Setup python + uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 + with: + python-version: "3.14" + + - name: Install uv + uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e + with: + python-version: 3.14 + + - name: Install project + run: uv sync --frozen + + - name: Generate KBase DOI list + run: uv run --frozen scripts/gen_kbase_doi_list.py + + - name: Create Pull Request with updated KBase DOI list + uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 + with: + token: ${{ secrets.GHCR_TOKEN || github.token }} + add-paths: | + src/docs/pages/kbase_dois.md + base: main + branch: update-kbase-dois + delete-branch: true + commit-message: "Update KBase FAIR Narratives DOI list" + title: "Update KBase FAIR Narratives DOI list" + body: | + Automated weekly update of `src/docs/pages/kbase_dois.md` generated by `scripts/gen_kbase_doi_list.py`. diff --git a/pyproject.toml b/pyproject.toml index a64f6b00..d4f0eafd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,44 +1,57 @@ [project] name = "credit-engine" version = "0.1.0" -description = "Add your description here" +description = "Standardised citation metadata for scientific datasets." readme = "README.md" requires-python = ">=3.12" dependencies = [ - "check-jsonschema>=0.33.0", - "linkml>=1.9.1", -] - -[dependency-groups] -dev = [ - "ruff>=0.11.0", -] -data_import = [ - "asteval>=1.0.6", - "dlt[deltalake,duckdb,parquet]>=1.10.0", - "httpx>=0.28.1", - "ipykernel>=6.29.5", - "json-merge-patch>=0.3.0", - "jsonpatch>=1.33", - "pyyaml>=6.0.2", - "streamlit>=1.45.0", - "vcrpy>=7.0.0", - "xmlschema>=4.0.1", -] -erdantic = [ - "erdantic>=1.1.0.post1", - "pygraphviz>=1.14", -] -docs = [ - "mkdocs-material>=9.6.9", - "mkdocs-mermaid2-plugin>=1.2.1", + "check-jsonschema>=0.38.2", + "dlt>=1.31.0", + "jsonschema[format]>=4.26.0", + "linkml>=1.12.1", + "linkml-runtime>=1.12.1", ] [tool.ruff] line-length = 120 -# Assume Python 3.12. -target-version = "py312" +# Assume Python 3.14. +target-version = "py314" + +# Allow autofix for all enabled rules (when `--fix`) is provided. +fixable = ["ALL"] +unfixable = [] + +# Exclude a variety of commonly ignored directories. +exclude = [ + "__pypackages__", + "_build", + ".bzr", + ".direnv", + ".eggs", + ".git-rewrite", + ".git", + ".github", + ".hg", + ".mypy_cache", + ".nox", + ".pants.d", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + "*.pyc", + "buck-out", + "build", + "deps", + "dist", + "node_modules", + "other_schema", + "python-coverage", + "sample_data", + "venv", +] [tool.ruff.lint] select = [ @@ -91,12 +104,12 @@ select = [ "TD", # flake8-todos "FIX", # flake8-fixme "ERA", # eradicate - # "PD", # pandas-vet + "PD", # pandas-vet "PGH", # pygrep-hooks "PL", # Pylint "TRY", # tryceratops "FLY", # flynt - # "NPY", # NumPy-specific rules + "NPY", # NumPy-specific rules "AIR", # Airflow "PERF", # Perflint "FURB", # refurb @@ -116,42 +129,23 @@ ignore = [ "E203", "E501", "ISC001", - "S101", ] -# Allow autofix for all enabled rules (when `--fix`) is provided. -fixable = ["ALL"] -unfixable = [] +[tool.ruff.lint.per-file-ignores] +"tests/**/*.py" = ["S101"] # use of assert +[tool.ruff.lint.mccabe] +# Flag errors (`C901`) whenever the complexity level exceeds 15. +max-complexity = 15 -# Exclude a variety of commonly ignored directories. -exclude = [ - "__pypackages__", - "_build", - ".bzr", - ".direnv", - ".eggs", - ".git-rewrite", - ".git", - ".github", - ".hg", - ".mypy_cache", - ".nox", - ".pants.d", - ".pytype", - ".ruff_cache", - ".svn", - ".tox", - ".venv", - "*.pyc", - "buck-out", - "build", - "deps", - "dist", - "node_modules", - "other_schema", - "python-coverage", - "sample_data", - "venv", +[dependency-groups] +dev = [ + "ruff>=0.17.2", +] +docs = [ + "mkdocs-material>=9.7.7", + "mkdocs-mermaid2-plugin>=1.2.3", +] +erd = [ + "erdantic>=1.2.1", ] -per-file-ignores = {} diff --git a/scripts/gen_kbase_doi_list.py b/scripts/gen_kbase_doi_list.py new file mode 100644 index 00000000..3c19f7d3 --- /dev/null +++ b/scripts/gen_kbase_doi_list.py @@ -0,0 +1,156 @@ +"""DataCite client. + +access to the DataCite DOI endpoint does not require authentication + +API documentation: https://support.datacite.org/docs/api +""" + +import datetime as dt +from collections.abc import Generator +from io import StringIO, TextIOWrapper +from pathlib import Path +from typing import Any, TextIO + +import dlt +from dlt.common.typing import TDataItem +from dlt.destinations import filesystem as fs_out +from dlt.sources.rest_api import rest_api_source + + +def has_required_keys(item: dict, required_keys: list) -> bool: + """Ensure that a dictionary has all required keys populated. + + :param item: dictionary to check + :type item: dict + :param required_keys: list of keys to check + :type required_keys: list + :return: True or False + :rtype: bool + """ + return all(item.get(key) for key in required_keys) + + +def datacite_prefix_endpoint(prefix: str) -> Generator[TDataItem, Any]: + """DataCite DOI endpoint for fetching DOIs by prefix. + + :param doi: prefix to retrieve + :type doi: str + :yield: REST API generator + :rtype: Generator[TDataItem, Any, None] + """ + yield from rest_api_source( + { + "client": {"base_url": "https://api.datacite.org/"}, + "resource_defaults": {"primary_key": "doi"}, + "resources": [ + { + "name": "doi_prefix_match", + "endpoint": { + "path": "dois", + "data_selector": "data[*].attributes", + "params": {"prefix": prefix, "sort": "-created", "affiliation": "true", "publisher": "true"}, + }, + }, + ], + } + ) + + +@dlt.transformer() +def extract_citation_data(item: dict[str, Any], fh: TextIO | TextIOWrapper) -> dict[str, Any]: + """Extract useful citation data from the item. + + :param item: citation data object from the datacite API. + :type item: dict[str, Any] + :return: cut-down citation data + :rtype: dict[str, Any] + """ + item["contributors"] = item["creators"] + item["contributors"] + for con in item["contributors"]: + if has_required_keys(con, ["familyName", "givenName"]): + con["citable"] = con.get("familyName") + " " + con.get("givenName")[:1] + else: + con["citable"] = con.get("name") + + if con.get("nameIdentifiers"): + for name_id in con.get("nameIdentifiers"): + if name_id.get("nameIdentifierScheme") == "ORCID": + # remove the full URL, replace with 'ORCID:' + con["orcid"] = name_id.get("nameIdentifier").replace("https://orcid.org/", "ORCID:") + break + + if fh and has_required_keys(item, ["doi", "titles", "contributors", "publicationYear", "updated"]): + print_row(fh, item) + else: + print(f"ERROR: doi:{item.get('doi', 'UNKNOWN')} is missing required fields") + + return item + + +def print_row(fh: TextIO | TextIOWrapper, item: dict[str, Any]) -> None: + """Print out DOI info to a file. + + :param fh: file handle to print to + :type fh: TextIO | TextIOWrapper + :param item: doi information in dictionary form + :type item: dict[str, Any] + """ + author_string = ", ".join(con.get("citable") for con in item.get("contributors", [])) + + fh.write( + f"| {item.get('doi')} | [{item.get('titles', {})[0]['title']}](https://dx.doi.org/{item.get('doi')})
{author_string} | {item.get('publicationYear')} | {item.get('updated')} |\n", + ) + + +def has_doi_changes(existing_content: str, new_content: str) -> bool: + """Compare existing and new markdown content, ignoring the 'Generated on' line. + + :param existing_content: current file content + :type existing_content: str + :param new_content: newly generated content + :type new_content: str + :return: True if content differs outside the 'Generated on' line + :rtype: bool + """ + existing_lines = [line for line in existing_content.splitlines() if not line.startswith("Generated on ")] + new_lines = [line for line in new_content.splitlines() if not line.startswith("Generated on ")] + return existing_lines != new_lines + + +def run_doi_update_pipeline(output_file: str) -> None: + """Run the pipeline to update the KBase DOI list. + + :param output_file: file to save the DOI info to. + :type output_file: str + """ + current_date = dt.datetime.now(tz=dt.UTC).date().isoformat() + buf = StringIO() + buf.write("# KBase FAIR Narratives\n") + buf.write(f"Generated on {current_date}\n\n") + buf.write("| DOI | Title, Authors | Published | Updated |\n|-----|----------------|-----------|---------|\n") + + # Create the pipeline + pipeline = dlt.pipeline( + pipeline_name="datacite_search_pipeline", + destination=fs_out(bucket_url="./out"), + dataset_name="datacite", + ) + extract_citation_data.bind(fh=buf) + # Run the pipeline + load_info = pipeline.run( + datacite_prefix_endpoint("10.25982") | extract_citation_data, + ) + print(load_info) + + new_content = buf.getvalue() + output_path = Path(output_file) + if output_path.exists() and not has_doi_changes(output_path.read_text(encoding="utf-8"), new_content): + print(f"No DOI changes detected in {output_file}; skipping file update.") + return + + output_path.write_text(new_content, encoding="utf-8") + print(f"Updated {output_file}.") + + +if __name__ == "__main__": + run_doi_update_pipeline("src/docs/pages/kbase_dois.md") diff --git a/src/docs/pages/kbase_dois.md b/src/docs/pages/kbase_dois.md index a83465cb..71f573a7 100644 --- a/src/docs/pages/kbase_dois.md +++ b/src/docs/pages/kbase_dois.md @@ -1,11 +1,35 @@ # KBase FAIR Narratives -Generated on 2025-06-24 +Generated on 2026-10-23 | DOI | Title, Authors | Published | Updated | |-----|----------------|-----------|---------| +| 10.25982/200198.21/3580370 | [Lines of Evidence Network Analysis of Yield-Associated Genes in Pennycress (Thlaspi arvense)](https://dx.doi.org/10.25982/200198.21/3580370)
Madrid G | 2026 | 2026-08-31T19:47:26Z | +| 10.25982/268294.9/3508092 | [Soil metagenomics umbrella narrative](https://dx.doi.org/10.25982/268294.9/3508092)
Schirmer A, Olfelt J, Bolterstein E, Nuss K, Conwell K, Dow E | 2026 | 2026-08-28T17:57:27Z | +| 10.25982/266974.4/3412610 | [Genome-resolved insights into microbial diversity and elemental cycling in Winogradsky columns](https://dx.doi.org/10.25982/266974.4/3412610)
Anthopoulos S, Boutwell K, Deans G, Glinkski, Jr. M, Zhong Z, Byambasuren K, Shrestha P, Miskelly A, Braden B, Faivre-Nigro R, Feliu K, Garlock E, Hotaling A, Kanaovicz M, Manning B, McGill K, Phoenix S, Ryu D, Solfrian J, Rodriguez-Bornot C, Yang J, Goff J | 2026 | 2026-08-14T20:18:29Z | +| 10.25982/264174.27/3378242 | [consortium_sutapa](https://dx.doi.org/10.25982/264174.27/3378242)
Sanyal S | 2026 | 2026-09-29T14:12:04Z | +| 10.25982/149351.18/3374972 | [Genomes_SET2_178 - Shared](https://dx.doi.org/10.25982/149351.18/3374972)
Sakkaf Z | 2023 | 2026-08-18T20:27:39Z | +| 10.25982/232191.29/3005254 | [Five PMI Isolates from Populus Deltoides and Populus Trichocarpa](https://dx.doi.org/10.25982/232191.29/3005254)
Crockett Z, Beals D, Nguyen A, Phan D | 2025 | 2026-07-08T17:32:06Z | +| 10.25982/243825.51/3374872 | [From Reads to Function Workshop - Milano 2026](https://dx.doi.org/10.25982/243825.51/3374872)
Ghisleni G, Dow E, Iovino T, Colman-Vega P, Dicesare A, Guanella E, Bacchi Y, Colombo A, Leccese M, Marzucchi M, Gorla M, Caracciolo A, Sala A, Makarycheva P, Rubrica S, Ferrier A, Armanni A, Fumagalli S, Wood-Charlson E, Bruno A | 2026 | 2026-06-25T14:55:02Z | +| 10.25982/250388.7/3025755 | [Post Wildfire Soil Bacterial MAGs and Metagenome Analysis](https://dx.doi.org/10.25982/250388.7/3025755)
Morrow M, Allen L | 2026 | 2026-06-19T15:16:37Z | +| 10.25982/251530.86/3363291 | [Integrative Modeling and Analysis of Fungal Central Carbon Metabolism](https://dx.doi.org/10.25982/251530.86/3363291)
Edirisinghe J, Lerma-Ortiz C, Liu F, Faria J, Cottingham R, Arkin A, Liu Q, Henry C | 2026 | 2026-05-12T13:51:15Z | +| 10.25982/255535.4/3097884 | [Characterization of Multiple Trichloroethene, cis-Dichloroethene and 1,1-Dichloroethene Degrading Propanotrophic Communities](https://dx.doi.org/10.25982/255535.4/3097884)
Faghihinezhad M, Eshghdoostkhatami Z, Cupples A | 2026 | 2026-04-29T15:20:06Z | +| 10.25982/219850.28/2997179 | [General Biology 2 Sugar Beet Lab - SU2025 - Final](https://dx.doi.org/10.25982/219850.28/2997179)
Schirmer A, Parikh K, Olfelt J, Bolterstein E, Nuss K, Conwell K | 2025 | 2026-03-30T15:09:19Z | +| 10.25982/3020148 | [MONet/1000 Soils metagenome pathway modelling narrative w/ auto batch import](https://dx.doi.org/10.25982/3020148)
Song Y, Ayala-Ortiz C, Graham E | 2026 | 2026-02-23T19:46:53Z | +| 10.25982/200311.171/3014786 | [Genome collection processing for “Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria”](https://dx.doi.org/10.25982/200311.171/3014786)
Favier A, Hernández-Terán A, Symons C, Rebolleda-Gómez M | 2026 | 2026-01-28T22:02:30Z | +| 10.25982/242870.6/3013398 | [Data Mining of Groundwater to Identify MAGs with Methane, Propane and Toluene Monooxygenases](https://dx.doi.org/10.25982/242870.6/3013398)
Cupples A, Del Cid M, Richard J | 2026 | 2026-01-23T19:27:09Z | +| 10.25982/234858.37/3012936 | [Metagenome-assembled genome of Salinarimonas species from the alkaliphilic alga Chlorella sp. SLA-04](https://dx.doi.org/10.25982/234858.37/3012936)
Arnold A, Miller I, Fields M, Gerlach R | 2026 | 2026-01-20T16:32:15Z | +| 10.25982/240632.11/3009289 | [KBase Narrative - 5 draft genomes of citrus-associated Bacillus isolates](https://dx.doi.org/10.25982/240632.11/3009289)
Vieira F | 2025 | 2025-12-19T22:02:00Z | +| 10.25982/227563.60/3004098 | [Tolumonas sp. WCU1](https://dx.doi.org/10.25982/227563.60/3004098)
O'Connell S, Hernandez A | 2025 | 2025-11-21T16:15:57Z | +| 10.25982/219679.217/2997510 | [Complete genome sequence of Sphingobium yanoikuyae strain CC4533](https://dx.doi.org/10.25982/219679.217/2997510)
Mitra M, Stanescu A | 2025 | 2025-10-06T17:06:38Z | +| 10.25982/217404.86/2589402 | [Bradyrhizobium sp. WCU1](https://dx.doi.org/10.25982/217404.86/2589402)
O'Connell S, Velásquez A, Simon J | 2025 | 2025-09-25T20:14:06Z | +| 10.25982/229295.9/2589424 | [Genomes of eight cultured microbes from soil sites in Wellesley, MA](https://dx.doi.org/10.25982/229295.9/2589424)
Biller S | 2025 | 2025-09-25T17:03:16Z | +| 10.25982/156785.278/2588866 | [Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database](https://dx.doi.org/10.25982/156785.278/2588866)
Schweitzer H, Tinker K, Barnhart E, Akob D, Crockett Z, Gulliver D | 2025 | 2026-07-15T17:30:27Z | +| 10.25982/221851.41/2584379 | [6051R & 6051S Assembly and Annotation](https://dx.doi.org/10.25982/221851.41/2584379)
Strong-Lundquist G, Robleto E | 2025 | 2025-08-22T13:27:50Z | +| 10.25982/206696.195/2570522 | [MAGs from alcoholic fermentation in sugarcane biorefineries](https://dx.doi.org/10.25982/206696.195/2570522)
Venturini A, Martins C, Gombert A | 2025 | 2025-06-27T17:28:31Z | | 10.25982/218406.47/2569606 | [Fermented Foods Microbial Genomes Database](https://dx.doi.org/10.25982/218406.47/2569606)
McDaniel E, Dutton R | 2025 | 2025-06-20T13:09:23Z | | 10.25982/187935.57/2565930 | [ISME Workshop - All Congo Genomes](https://dx.doi.org/10.25982/187935.57/2565930)
Allen B | 2025 | 2025-05-15T02:15:24Z | -| 10.25982/200793.58/2556864 | [TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria](https://dx.doi.org/10.25982/200793.58/2556864)
Tothero G, Weisenhorn P, Liu F, Faria J, Henry C, Chan C | 2025 | 2025-04-17T02:23:18Z | +| 10.25982/33233.606/1831502 | [Genome Extraction from Shotgun Metagenome Sequence Data](https://dx.doi.org/10.25982/33233.606/1831502)
Chivian D, Jungbluth S, Dehal P, Canon R, Allen B, Clark M, Gu T, Land M, Price G, Riehl W, Sneddon M, Sutormin R, Zhang Q, Cottingham R, Henry C, Arkin A | 2021 | 2025-06-01T01:01:23Z | +| 10.25982/187935.57/2565930 | [ISME Workshop - All Congo Genomes](https://dx.doi.org/10.25982/187935.57/2565930)
Allen B | 2025 | 2025-05-15T02:15:24Z | | 10.25982/189485.18/2538685 | [Seven soil endospore forming bacteria from campus woodland fragments](https://dx.doi.org/10.25982/189485.18/2538685)
McLoon A, Cucca A, Gardner L, Higgins M, Rigby C, Rigby C, Gerbasi F, Lunman A, Mondelo V, Kronau L, Gejo J, Le J, Naef M, Spiliotis C, Churan G, Barker J, Maune K | 2025 | 2025-03-27T02:26:07Z | | 10.25982/175980.54/2520041 | [General Biology 2 Sugar Beet Lab - Spring 24](https://dx.doi.org/10.25982/175980.54/2520041)
Schirmer A, Parikh K | 2025 | 2025-02-21T03:37:31Z | | 10.25982/165213.26/2519695 | [RWRtoolkit Narrative](https://dx.doi.org/10.25982/165213.26/2519695)
Kainer D, Lane M, Sullivan K, Miller J, Cashman M, Morgan M, Cliff A, Romero J, Walker A, Blair D, Chhetri H, Wang Y, Pavicic M, Furches A, Noshay J, Drake M, Landry N, Ireland A, Missaoui A, Kang Y, Sedbrook J, Dehal P, Canon S, Jacobson D | 2024 | 2025-02-20T03:37:28Z | @@ -15,19 +39,18 @@ Generated on 2025-06-24 | 10.25982/193023.110/2479104 | [KBase Narrative - Complete genome sequence of a novel Microbacterium sp. strain Clip185.](https://dx.doi.org/10.25982/193023.110/2479104)
Mitra M, Stanescu A | 2024 | 2024-12-05T03:11:27Z | | 10.25982/166913.44/2476642 | [KBase Narrative - van den Bergh et al](https://dx.doi.org/10.25982/166913.44/2476642)
Rocha G, Van Den Bergh S | 2024 | 2024-11-12T03:08:25Z | | 10.25982/197146.10/2475943 | [RNA-Seq analysis of nine tRNA-Modification deficient mutants in E. coli](https://dx.doi.org/10.25982/197146.10/2475943)
De Crécy-Lagard V, Babor J, Bacusmo J, Dedon P | 2024 | 2024-11-08T03:13:34Z | -| 10.25982/185119.92/2404572 | [Luteolibacter sp. strain Populi](https://dx.doi.org/10.25982/185119.92/2404572)
Allen B, Podar M | 2024 | 2024-07-20T02:10:04Z | -| 10.25982/186528.9/2404396 | [KBase Narrative - Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley MA](https://dx.doi.org/10.25982/186528.9/2404396)
Biller S | 2024 | 2024-08-16T02:05:47Z | | 10.25982/157793.280/2368552 | [KBase Narrative - 13 draft genomes of Bacillus from HLB-impacted citrus trees](https://dx.doi.org/10.25982/157793.280/2368552)
Vieira F, Blacutt A, Drozd C, Viravathana P, Ginnan N, Roper C | 2024 | 2024-10-24T08:55:21Z | +| 10.25982/186528.9/2404396 | [KBase Narrative - Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley MA](https://dx.doi.org/10.25982/186528.9/2404396)
Biller S | 2024 | 2024-08-16T02:05:47Z | +| 10.25982/185119.92/2404572 | [Luteolibacter sp. strain Populi](https://dx.doi.org/10.25982/185119.92/2404572)
Allen B, Podar M | 2024 | 2024-07-20T02:10:04Z | | 10.25982/169030.42/2345706 | [KBase Narrative - Methylobacterium fujisawaense Strain C14 Genomic Sequence](https://dx.doi.org/10.25982/169030.42/2345706)
Kiledal E, Moxley I, Shevchenko O, Goff J, Maresca J | 2024 | 2024-06-14T02:12:57Z | +| 10.25982/95510.53/2310383 | [KBase Narrative - C. roseus Tissue Specificity Analysis using Góngora-Castillo Transcripts and Franke v2 Genome](https://dx.doi.org/10.25982/95510.53/2310383)
Cole-Osborn L, MCCallan S, Prifti O, Abu R, Sjoelund V, Lee-Parsons C | 2022 | 2024-05-18T21:51:46Z | +| 10.25982/135835.33/2203552 | [KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site](https://dx.doi.org/10.25982/135835.33/2203552)
Szink E, Goff J, Durrence K, Lui L, Nielsen T, Kuehl J, Hunt K, Chandonia J, Thorgersen M, Poole F, Stahl D, Chakraborty R, Arkin A, Adams M | 2023 | 2024-05-07T02:10:50Z | | 10.25982/179975.10/2345704 | [KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures](https://dx.doi.org/10.25982/179975.10/2345704)
Goff J, Hahn C, Ingrassia R, Tiyapun C, Waldschmidt G, Moxley I, Smith E, Marini M, Shevchenko O, Maresca J | 2024 | 2024-05-07T02:09:20Z | +| 10.25982/95771.20/1828592 | [The moderately defficient enzyme: Catalysis-related damage in vivo and its repair](https://dx.doi.org/10.25982/95771.20/1828592)
Henry C | 2021 | 2024-04-16T02:03:50Z | | 10.25982/138721.208/2336591 | [KBase Narrative - Timberlake Metagenomes](https://dx.doi.org/10.25982/138721.208/2336591)
De Mesquita C, Ciapina W, Ardón M, Tringe S | 2024 | 2024-04-13T02:43:09Z | | 10.25982/157568.747/2335480 | [KBase Narrative - Metabolic_reconstruction_ETDI_mangrove](https://dx.doi.org/10.25982/157568.747/2335480)
Laux M, Ciapina L, Carvalho F, Vasconcelos A | 2024 | 2024-04-11T18:04:44Z | | 10.25982/175564.2/2329279 | [KBase Narrative - StRoNG Net Part 2: Genome Analysis - Student - Static](https://dx.doi.org/10.25982/175564.2/2329279)
Schirmer A | 2024 | 2024-03-29T02:47:22Z | | 10.25982/175568.4/2329277 | [KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy](https://dx.doi.org/10.25982/175568.4/2329277)
Schirmer A, Whitham J | 2024 | 2024-03-29T02:47:18Z | -| 10.25982/90888.1452/2327015 | [KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Sequence quality filtration & Assembly-](https://dx.doi.org/10.25982/90888.1452/2327015)
Plominsky A | 2024 | 2024-03-26T02:48:12Z | -| 10.25982/138628.97/2327013 | [KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential-](https://dx.doi.org/10.25982/138628.97/2327013)
Plominsky A | 2024 | 2024-03-26T02:48:27Z | -| 10.25982/174276.9/2324582 | [KBase Narrative - Formation of a constructed microbial community in a nutrient rich environment indicates bacterial interspecific competition](https://dx.doi.org/10.25982/174276.9/2324582)
Wang J, Appidi M, Burdick L, Abraham P, Hettich R, Pelletier D, Doktycz M | 2024 | 2024-03-19T02:32:10Z | -| 10.25982/95510.53/2310383 | [KBase Narrative - C. roseus Tissue Specificity Analysis using Góngora-Castillo Transcripts and Franke v2 Genome](https://dx.doi.org/10.25982/95510.53/2310383)
Cole-Osborn L, MCCallan S, Prifti O, Abu R, Sjoelund V, Lee-Parsons C | 2022 | 2024-05-18T21:51:46Z | | 10.25982/138628.97/2327013 | [KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential-](https://dx.doi.org/10.25982/138628.97/2327013)
Plominsky A | 2024 | 2024-03-26T02:48:27Z | | 10.25982/90888.1452/2327015 | [KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Sequence quality filtration & Assembly-](https://dx.doi.org/10.25982/90888.1452/2327015)
Plominsky A | 2024 | 2024-03-26T02:48:12Z | | 10.25982/171033.8/2309719 | [KBase Narrative - Lachnospiraceae sp. C1.1 genome](https://dx.doi.org/10.25982/171033.8/2309719)
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