orfdata 0.6.0__tar.gz → 0.8.0__tar.gz

{orfdata-0.6.0 → orfdata-0.8.0}/MANIFEST.in

@@ -1,3 +1,5 @@
 include lint.sh test.sh deploy.sh
 recursive-include docs *.md
 recursive-include tests *.py *.json *.md *.tsv *.fasta
+recursive-include tests/data/copy *.xlsx *.gz *.soft *.xml *.pdf
+recursive-include tests/data/storage *.sqlite

{orfdata-0.6.0/orfdata.egg-info → orfdata-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.6.0
+Version: 0.8.0
 Summary: Reference open reading frames and experimental translation evidence on annotated transcripts
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -102,9 +102,10 @@ new experimental ORF catalogues. [Species and reference identity](docs/species.m
 Install with `pip install orfdata[pyensembl]`. See the
 [measurement API](docs/measurements.md) for native units, explicit samples and
 assays, and DataCache-managed downloads. Downloadable
-[human, mouse and dog protein abundance](docs/pfizer-protein.md) uses the same
-species-scoped API. These canonical-search protein groups do not establish
+[human, mouse and dog protein abundance](docs/pfizer-protein.md) and
+[yeast calibrated protein/RNA abundance](docs/copy-yeast.md) use the same
+species-scoped API. These canonical-search measurements do not establish
 noncanonical ORF abundance. The
 [quantitative, multispecies data roadmap](https://github.com/openvax/orfdata/issues/3)
-tracks RNA abundance, ribosome occupancy, yeast absolute quantification and
+tracks further RNA abundance, ribosome occupancy, absolute quantification and
 additional protein data releases.

{orfdata-0.6.0 → orfdata-0.8.0}/README.md

@@ -75,9 +75,10 @@ new experimental ORF catalogues. [Species and reference identity](docs/species.m
 Install with `pip install orfdata[pyensembl]`. See the
 [measurement API](docs/measurements.md) for native units, explicit samples and
 assays, and DataCache-managed downloads. Downloadable
-[human, mouse and dog protein abundance](docs/pfizer-protein.md) uses the same
-species-scoped API. These canonical-search protein groups do not establish
+[human, mouse and dog protein abundance](docs/pfizer-protein.md) and
+[yeast calibrated protein/RNA abundance](docs/copy-yeast.md) use the same
+species-scoped API. These canonical-search measurements do not establish
 noncanonical ORF abundance. The
 [quantitative, multispecies data roadmap](https://github.com/openvax/orfdata/issues/3)
-tracks RNA abundance, ribosome occupancy, yeast absolute quantification and
+tracks further RNA abundance, ribosome occupancy, absolute quantification and
 additional protein data releases.

orfdata-0.8.0/docs/copy-yeast.md

@@ -0,0 +1,109 @@
+# Yeast protein and RNA abundance
+
+`copy-yeast-abundance` imports [Lawless et al., CoPY (2016)](https://doi.org/10.1074/mcp.M115.054288)
+through the same dataset API as human, mouse and dog. It includes calibrated
+protein and peptide quantities, label-free estimates and RNA from budding yeast
+grown in glucose-limited chemostats. The strain is EUROSCARF Y11335 BY4742,
+with the reported genotype retained on each sample.
+
+```sh
+pip install 'orfdata[data]'
+orfdata datasets info copy-yeast-abundance
+orfdata datasets download copy-yeast-abundance
+orfdata datasets pairs copy-yeast-abundance --basis condition_aggregate
+```
+
+The release contains 69,125 observations in a roughly 14 MB compressed download
+(168 MB installed). Downloads are explicit and checksum-verified through
+DataCache. Queries work offline after installation.
+
+| Source measurements | Coverage | Interpretation |
+|---|---:|---|
+| QconCAT SRM protein summaries | 1,903 rows | 1,167 quantified; 668 upper bounds; 68 unquantifiable |
+| SRM peptide observations | 3,836 rows × four cultures and author median | Protein-specific isotope standards; copies/cell, classification and uncertainty |
+| Aggregate RNA | 6,581 labels × FPKM and estimated copies/cell | Counts aggregated before FPKM; copies assume 60,000 total mRNAs/cell |
+| Individual RNA libraries | Four × 7,137 tracking IDs | Native FPKM, 95% confidence interval and Cufflinks status |
+| Label-free estimates | 3,166 rows × two methods | Q-Exactive internal-standard Top3 and SAX total-protein scaling remain separate |
+
+The 55 joined SRM protein groups retain their combined attribution. Label-free
+identities also remain groups because full membership is unresolved. Two rows
+share the label YNL239W; both survive unchanged. Upper bounds have
+`status="below_detection"`, `value=None` and a `detection_limit`; missing and
+unquantifiable values never become zeros. Author-calibrated SRM estimates have
+`origin="observed"`; the RNA copies/cell conversion has `origin="derived"`
+with its original FPKM input and calibration assumption.
+
+The QconCAT FASTA contains 93 synthetic calibration standards, not native yeast
+proteins. Four reported peptides do not match their assigned standard; their
+measurements retain an explicit validation flag. See [source reconciliation #34](https://github.com/openvax/orfdata/issues/34).
+Raw transitions and light/heavy ratios are not supplied in the processed
+workbook. SRM raw data are identified by PASS00717; PXD002694 is the label-free
+deposit. RNA is from GSE73898. Cufflinks LOWDATA rows retain their original
+positive/zero estimates and confidence bounds in provenance, while the query
+value remains `not_measured` because reliable quantification is unresolved.
+
+## Comparing RNA and protein
+
+The paper supports same-cell measurements at the source-cohort level. The
+individual MS-to-RNA replicate crosswalk is unresolved, so comparisons require
+explicit `condition_aggregate` selection. Replicate numbers alone never join
+samples. Label-free methods have different calibrations and no inferred RNA pair.
+
+```python
+from orfdata import DatasetRegistry
+
+dataset = DatasetRegistry().open("copy-yeast-abundance")
+match = next(
+    m for m in dataset.matched_measurements(allowed_bases=["condition_aggregate"])
+    if m.relation.left.identifier == "YML035C"  # AMD1, yeast source context
+)
+protein = match.right[0]  # 3203.943997 copies/cell; author SRM estimate
+rna = next(m for m in match.left if m.unit == "copies/cell")  # ~2.11665
+ratio = match.ratio(
+    protein, rna, measurement_id="AMD1:protein-per-RNA",
+    method="native calibrated protein / estimated RNA",
+    normalization={"assumed_total_mrna_per_cell": 60000, "level": "source cohort"},
+)
+print(ratio.value, ratio.unit, ratio.derivation)
+```
+
+The ratio is conditional on the RNA calibration. It is neither a translation
+rate nor ribosome occupancy. Group relationships cannot yield an individual
+protein ratio. All quantities keep their source units and assumptions.
+
+## References and other species
+
+Both yeast contexts carry taxon 4932 and pinned source hashes. The historical
+SGD/Bowtie genome and annotation releases are unspecified; assembly, annotation
+version and reference strain remain null. These source labels support canonical
+gene/protein relationships but cannot bind a current PyEnsembl transcript until
+a reference mapping is validated. Sample BY4742 strain is separate from the
+unknown reference-genome strain. This dataset does not establish which yeast
+noncanonical ORFs were searched, expressed or absent.
+
+For cross-species comparisons, supply independently validated, pinned orthology
+records rather than joining gene names. For example, with an installed mammal
+RNA dataset and a curated JSON list of `OrthologyMapping` records:
+
+```python
+import json
+from orfdata import OrthologyMapping, compare_orthologs
+
+with open("curated-yeast-mammal-orthology.json") as handle:
+    mappings = [OrthologyMapping.from_dict(row) for row in json.load(handle)]
+for comparison in compare_orthologs(dataset, mammal_rna_dataset, mappings):
+    print(comparison.left, comparison.right)  # Separate original measurements
+```
+
+The mapping must name both exact references, its release, source checksum,
+cardinality and confidence. No expression or protein-existence evidence transfers
+between species, and different cultures/calibrations remain different experiments.
+See [pairing and orthology](pairing.md).
+
+To rebuild the release from the pinned public workbook, standards, metadata and
+four RNA files, install `orfdata[data,build-data]` and run
+`orfdata datasets build copy-yeast-abundance`. Python uses
+`DatasetRegistry().build("copy-yeast-abundance")`. Local verified inputs can be
+supplied with repeated `--source-path ASSET=PATH` or `source_paths={...}`.
+The workbook and standards use stable versioned PMC objects; the dynamically
+generated EuropePMC ZIP is not used as a content identity.

{orfdata-0.6.0 → orfdata-0.8.0}/docs/measurements.md

@@ -145,4 +145,5 @@ arbitrary other taxa use the same schema. The core API needs neither pandas nor
 PyArrow. Optional `orfdata[columnar]` enables `dataset.export_parquet(path)`;
 query columns accompany full measurement JSON, preserving exact values and
 provenance even when a floating-point analysis column cannot represent an
-integer exactly.
+integer exactly. [Compact storage and compatibility](storage.md) describes
+new SQLite v4 writes, legacy readers and actual-source size/query benchmarks.

orfdata-0.8.0/docs/storage.md

@@ -0,0 +1,45 @@
+# Quantitative storage
+
+ORFdata 0.8 writes compact SQLite storage version 4. `Measurement`,
+`QuantitativeDataset`, the registry and CLI keep the same public records and
+query semantics. Human, mouse, dog, yeast and arbitrary taxa retain separate
+reference-scoped identities.
+
+References, targets and assays are stored once and addressed by internal integer
+keys. Measurements retain their values and metadata; repeated required fields
+are reconstructed from indexed columns and the dataset manifest. Fields equal
+to the fixed version-4 defaults are omitted from stored JSON and restored on read.
+Zeros, nulls, censoring, uncertainty, nested provenance and derived inputs retain
+their meaning. Foreign keys prevent cross-reference target/assay assignments.
+Internal integer keys never appear as public biological identifiers.
+
+Published storage versions 1, 2 and 3 remain readable. There is no automatic
+migration or replacement of downloaded artifacts. A new source rebuild can use
+a different storage layout and therefore a different file checksum while
+returning the same records. Registry downloads always verify the exact published
+artifact's hash; source builds retain their own DataCache receipts.
+
+The implementation streams observations and bounds its target cache to 131,072
+entries. SQLite index statistics are populated during creation so a narrow
+target query can use the target index instead of scanning an entire reference.
+Raw SQL table layouts are internal; use the Python/CLI query and export APIs.
+
+## Actual-source benchmark
+
+The first 100,000 rows of the native Pfizer/GEO RNA table contain four dog
+libraries and 30,941 genes, including measured zeros. Source gzip SHA-256:
+`a22780f92ffd0a028e30fe3392d73d01f787eb5a62b2043e8d26940191cbac70`.
+This is a storage benchmark slice, not a newly released experimental dataset.
+
+| Measurement | Storage v3 | Storage v4 |
+|---|---:|---:|
+| Installed size | 121.6 MB | 38.6 MB |
+| Gzip size | 13.4 MB | 7.5 MB |
+| Build time | 8.90 s | 4.28 s |
+| One-gene query (four results) | 135 ms | 1.5 ms |
+| Peak build RSS | 39.8 MB | 52.1 MB |
+
+All 100,000 reconstructed observations were compared field for field. Timings
+are local measurements on Python 3.12, not cross-machine guarantees; the bounded
+target cache trades some memory for repeated-target lookup speed. Legacy tests
+also use actual databases written by ORFdata 0.3.0, 0.4.0 and 0.5.0.

{orfdata-0.6.0 → orfdata-0.8.0}/orfdata/data/datasets.json

@@ -384,5 +384,364 @@
         }
       }
     }
+  },
+  "copy-yeast-abundance": {
+    "default_version": "2026-10-12.1",
+    "versions": {
+      "2026-10-12.1": {
+        "manifest": {
+          "dataset_id": "copy-yeast-abundance",
+          "version": "2026-10-12.1",
+          "title": "CoPY yeast calibrated SRM protein/peptide abundance and source-cohort RNA",
+          "references": [
+            {
+              "taxon_id": 4932,
+              "species": "yeast",
+              "genome_build": null,
+              "annotation_name": "sgd",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": null,
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": "22fa0a6143fb2f0d1fc350d63988b47cc5b62608839a5af3408201589b9329f8"
+            },
+            {
+              "taxon_id": 4932,
+              "species": "yeast",
+              "genome_build": null,
+              "annotation_name": "sgd",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": null,
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": "94c41f50b5d90255d10d47a567febc8011fde72dcd851003127082ac2ea92b69"
+            }
+          ],
+          "sources": [
+            {
+              "asset_id": "workbook.xlsx",
+              "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4824857.1/10.1074_M115.054288_mcp.M115.054288-4.xlsx",
+              "sha256": "22fa0a6143fb2f0d1fc350d63988b47cc5b62608839a5af3408201589b9329f8",
+              "size": 1236663,
+              "access_terms": "Lawless et al. 2016, CC-BY-4.0",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016; PMC4824857 version 1",
+                "source_name": "10.1074_M115.054288_mcp.M115.054288-4.xlsx"
+              }
+            },
+            {
+              "asset_id": "qconcat.fasta",
+              "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4824857.1/10.1074_M115.054288_mcp.M115.054288-5.txt",
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+              "size": 65604,
+              "access_terms": "Lawless et al. 2016, CC-BY-4.0",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016; PMC4824857 version 1",
+                "source_name": "10.1074_M115.054288_mcp.M115.054288-5.txt"
+              }
+            },
+            {
+              "asset_id": "pmc-metadata.json",
+              "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4824857.1/PMC4824857.1.json",
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+              "size": 1997,
+              "access_terms": "Lawless et al. 2016, CC-BY-4.0",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016; PMC4824857 version 1",
+                "source_name": "PMC4824857.1.json"
+              }
+            },
+            {
+              "asset_id": "paper.xml",
+              "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4824857.1/PMC4824857.1.xml",
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+              "size": 170874,
+              "access_terms": "Lawless et al. 2016, CC-BY-4.0",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016; PMC4824857 version 1",
+                "source_name": "PMC4824857.1.xml"
+              }
+            },
+            {
+              "asset_id": "methods.pdf",
+              "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4824857.1/10.1074_M115.054288_mcp.M115.054288-1.pdf",
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+              "access_terms": "Lawless et al. 2016, CC-BY-4.0",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016; PMC4824857 version 1",
+                "source_name": "10.1074_M115.054288_mcp.M115.054288-1.pdf"
+              }
+            },
+            {
+              "asset_id": "geo-series.soft",
+              "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73898&targ=self&form=text&view=full",
+              "sha256": "94c41f50b5d90255d10d47a567febc8011fde72dcd851003127082ac2ea92b69",
+              "size": 2321,
+              "access_terms": "NCBI places no restrictions on GEO data use or distribution; retain source attribution",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
+              "asset_id": "GSM1905474_KL9_fpkm.txt.gz",
+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1905nnn/GSM1905474/suppl/GSM1905474_KL9_fpkm.txt.gz",
+              "sha256": "eefad9dd94eb1c23822151fc5c13622850f827219e5324527de848e9bb893735",
+              "size": 251872,
+              "access_terms": "NCBI places no restrictions on GEO data use or distribution; retain source attribution",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
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+              "access_terms": "NCBI places no restrictions on GEO data use or distribution; retain source attribution",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
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+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1905nnn/GSM1905476/suppl/GSM1905476_KL10_fpkm.txt.gz",
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+              "size": 252094,
+              "access_terms": "NCBI places no restrictions on GEO data use or distribution; retain source attribution",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
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+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
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+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1905nnn/GSM1905478/suppl/GSM1905478_KL11_fpkm.txt.gz",
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+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
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+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
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+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1905nnn/GSM1905479/suppl/GSM1905479_KL12_fpkm.txt.gz",
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+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            },
+            {
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+              "access_terms": "NCBI places no restrictions on GEO data use or distribution; retain source attribution",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Lawless et al. 2016, GSE73898"
+              }
+            }
+          ],
+          "citations": [
+            "https://doi.org/10.1074/mcp.M115.054288",
+            "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73898",
+            "https://www.peptideatlas.org/PASS/PASS00717",
+            "https://www.ebi.ac.uk/pride/archive/projects/PXD002694"
+          ],
+          "assay_kinds": [
+            "targeted_ms",
+            "digest_ms",
+            "rna_seq"
+          ],
+          "coverage": {
+            "sheet_rows": {
+              "ProteinQuant": 1903,
+              "PeptideQuant": 3836,
+              "RNA": 6581,
+              "LabelFree": 3166
+            },
+            "protein_classes": {
+              "AA": 532,
+              "AB": 388,
+              "AC": 243,
+              "A-": 4,
+              "BB": 401,
+              "BC": 266,
+              "B-": 1,
+              "CC": 65,
+              "C-": 3
+            },
+            "standard_sequences": 93,
+            "standard_validation": {
+              "exact_subsequence": 3832,
+              "peptide_not_in_standard": 4
+            },
+            "quantified_protein_or_groups": 1167,
+            "upper_bound_protein_or_groups": 668,
+            "unquantifiable_protein_or_groups": 68,
+            "joined_srm_protein_groups": 55,
+            "label_free_unique_labels": 3165,
+            "label_free_duplicate_labels": {
+              "YNL239W": 2
+            },
+            "raw_rna_rows": 28548,
+            "raw_rna_lowdata_rows": 296,
+            "sample_pairing": "Source-cohort aggregate RNA/SRM only; individual MS/RNA replicate correspondence unresolved",
+            "reference_limits": "Historical SGD/Bowtie build and annotation release unspecified; source-only contexts cannot bind current PyEnsembl transcripts",
+            "standard_limits": "Four peptide rows do not match their reported synthetic standard; preserve quantities and explicit validation status",
+            "nc_orf_search": "Canonical targets; noncanonical ORF search not established; no ORF absence claim",
+            "excluded": "qconcatsummary redundant design/count table; raw transitions and light/heavy ratios not in workbook; no ribosome profiling"
+          },
+          "processing": {
+            "importer": "copy-yeast-v1",
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+                "title": "yeast RNA-seq fast BioRep2",
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+                "title": "yeast RNA-seq fast BioRep3",
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+                "statuses": {
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+                "metadata_asset": "GSM1905479.soft",
+                "biological_replicate": "4",
+                "title": "yeast RNA-seq fast BioRep4",
+                "rows": 7137,
+                "statuses": {
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+            ],
+            "aggregation": "Published RNA counts aggregated before FPKM; not a mean of per-replicate FPKM",
+            "calibrations": {
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+              "RNA": "FPKM/sum(FPKM)*60000 assumed mRNA/cell",
+              "Qexactive": "Top3; 50 fmol P00489 and 400000 cells",
+              "SAX": "Top3; assumed 60000000 protein molecules/cell"
+            },
+            "unresolved": [
+              "Exact historical native sequence reference",
+              "Individual cross-assay biological replicate mapping",
+              "Label-free full protein-group membership"
+            ],
+            "operations": [
+              "Preserve native rows, measured zeros, bounds and missingness",
+              "Retain distinct calibration and quality flags",
+              "Keep grouped targets unresolved",
+              "Attach cohort-only RNA/protein relations"
+            ]
+          },
+          "schema": "orfdata.measurements.v1"
+        },
+        "distribution": {
+          "access_terms": "Lawless et al. 2016 workbook and QconCAT annotations: CC-BY-4.0. GEO numerical data: unrestricted NCBI reuse with author attribution. ORFdata transformation code: Apache-2.0.",
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+          "data_release": "data-copy-yeast-2026-10-12.1"
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   }
 }