orfdata 0.5.0__tar.gz → 0.7.0__tar.gz

orfdata-0.7.0/MANIFEST.in

@@ -0,0 +1,4 @@
+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

{orfdata-0.5.0/orfdata.egg-info → orfdata-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.5.0
+Version: 0.7.0
 Summary: Reference open reading frames and experimental translation evidence on annotated transcripts
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -95,12 +95,17 @@ RNA products. Reference evidence stays separate from evidence for a variant or
 fusion. See the [API and integration guide](docs/reference.md).
 
 The catalogue API supports other species, with explicit species and assembly
-checks. **Bundled experimental evidence is currently human-only**. Offline tests
+checks. **The bundled experimental ORF catalogue is currently human-only**. Offline tests
 bind real human, mouse, dog and yeast reference slices; those fixtures are not
 new experimental ORF catalogues. [Species and reference identity](docs/species.md).
 
 Install with `pip install orfdata[pyensembl]`. See the
 [measurement API](docs/measurements.md) for native units, explicit samples and
-assays, and DataCache-managed downloads, and the
+assays, and DataCache-managed downloads. Downloadable
+[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)
-for upcoming RNA abundance, ribosome occupancy and protein data releases.
+tracks further RNA abundance, ribosome occupancy, absolute quantification and
+additional protein data releases.

{orfdata-0.5.0 → orfdata-0.7.0}/README.md

@@ -68,12 +68,17 @@ RNA products. Reference evidence stays separate from evidence for a variant or
 fusion. See the [API and integration guide](docs/reference.md).
 
 The catalogue API supports other species, with explicit species and assembly
-checks. **Bundled experimental evidence is currently human-only**. Offline tests
+checks. **The bundled experimental ORF catalogue is currently human-only**. Offline tests
 bind real human, mouse, dog and yeast reference slices; those fixtures are not
 new experimental ORF catalogues. [Species and reference identity](docs/species.md).
 
 Install with `pip install orfdata[pyensembl]`. See the
 [measurement API](docs/measurements.md) for native units, explicit samples and
-assays, and DataCache-managed downloads, and the
+assays, and DataCache-managed downloads. Downloadable
+[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)
-for upcoming RNA abundance, ribosome occupancy and protein data releases.
+tracks further RNA abundance, ribosome occupancy, absolute quantification and
+additional protein data releases.

orfdata-0.7.0/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-0.5.0 → orfdata-0.7.0}/docs/measurements.md

@@ -6,8 +6,9 @@ proteins, protein groups and peptides. A measurement stays at the resolution
 the experiment supports. Parent-gene RNA abundance is useful context for an ORF;
 it is not a separate measurement of each ORF in that gene.
 
-Install `orfdata[data]` to manage datasets. The initial 0.3 registry is empty;
-the [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks source
+Install `orfdata[data]` to manage datasets. The registry includes downloadable
+[Pfizer/Oziolor human, mouse and dog protein summaries](pfizer-protein.md);
+the [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks further
 imports. The bundled human ORF evidence catalogue remains available offline.
 Its pooled PSM counts describe spectra, not sample-level protein abundance.
 
@@ -130,6 +131,12 @@ definitions = {
 ```
 
 CLI users can supply this JSON with `orfdata datasets --registry FILE ...`.
+
+Rebuild supported releases from their pinned original inputs with
+`registry.build(name, version, source_paths={"asset_id": "/local/file"})` or
+`orfdata datasets build NAME --source-path ASSET=PATH`. Local overrides still
+require the published hashes. Rebuilds use a separate import cache and preserve
+installed releases. Unsupported source importers fail explicitly.
 `ORFDATA_CACHE`, then `OPENVAX_DATA_CACHE`, then the platform's OpenVax cache
 select the root. ORFdata owns its `orfdata/` child. Release cache identities
 include manifest/reference and content hashes. SQLite partitions every table

orfdata-0.7.0/docs/pfizer-protein.md

@@ -0,0 +1,71 @@
+# Human, mouse and dog protein abundance
+
+The [Oziolor et al. atlas](https://doi.org/10.1038/s41597-026-07512-9) provides
+parallel TMT protein measurements. ORFdata keeps each species in a separate
+dataset, using the same samples, assays, measurements and query API.
+
+| Dataset | Reported protein groups | Source channels | Source rows |
+|---|---:|---:|---:|
+| `pfizer-atlas-human-protein` | 10,352 | 37 | 325,702 |
+| `pfizer-atlas-mouse-protein` | 12,124 | 63 | 615,991 |
+| `pfizer-atlas-dog-protein` | 9,929 | 38 | 313,263 |
+
+Release `2026-10-12.1` contains the complete March 23, 2026 summary tables from
+MassIVE MSV000099729, MSV000099754 and MSV000099744, respectively. Each source
+row contributes two observations: native `iBAQ` and `rIBAQ`. Neither is calibrated
+copies per cell. These are pooled tissue samples; rodent condition labels also
+include sex. Channels and technical runs do not count as independent donors.
+
+```sh
+pip install 'orfdata[data]'
+orfdata datasets list --species dog
+orfdata datasets download pfizer-atlas-dog-protein
+orfdata datasets query pfizer-atlas-dog-protein --quantity protein_abundance
+```
+
+```python
+from orfdata import DatasetRegistry, ScopedTarget
+
+registry = DatasetRegistry()
+dataset = registry.open("pfizer-atlas-dog-protein")  # After explicit download.
+reference, = dataset.manifest.references
+group = ScopedTarget(reference, "protein_group", "A0A0A0MPB0", "MSV000099744:ProteinGroup")
+for value in dataset.measurements(target=group):
+    print(value.sample_id, value.unit, value.value, value.status)
+```
+
+Every target retains its species and the checksum of the deposited UniProt
+search FASTA. The original genomic assembly and UniProt release are unknown.
+They stay unknown; a future annotation mapping must be explicit and validated.
+Group representatives can be inspected through `reference_mappings()`, but their
+lookup does not establish all group members. Opting into unresolved mapped
+views keeps the original group measurement visible, without assigning its value
+to an individual protein. No RNA pairings are inferred in this release.
+
+Source `NA` values remain missing and numeric zeros remain measured zeros.
+Absent group/channel combinations have no observation. For dog, 64,039 combinations
+are absent and eight reported rows contain `NA`, reproducing the existing
+64,047 missing iBAQ matrix cells. Each value retains its source line, column,
+original numeric text, representative, normalization sum and native `Abundance`
+field. Nonfinite transformed strings such as `-Inf` are kept as provenance only.
+
+These searches used UniProt sequences without spliced isoforms. Coverage does
+not establish that an unreported ncORF was searched or absent, nor does bulk
+tissue MS establish MHC presentation. The article and deposit disagree on the
+instrument name; that discrepancy remains explicit in assay metadata.
+
+Downloads are 87.3 MB (human), 154.8 MB (mouse) and 84.4 MB (dog). Installed
+SQLite files occupy 1.46 GB, 2.72 GB and 1.40 GB, respectively. Queries stream
+observations; they do not load the entire file or a dense matrix into memory.
+
+Source tables are CC0 according to the MassIVE deposits; UniProt search records
+retain UniProt Consortium attribution and CC-BY-4.0 terms. Both sources have
+pinned hashes and sizes. The data artifact is separate from the Python package.
+Discovery and installed queries work offline. `download` verifies and installs
+the compressed artifact; it does not fetch the large vendor search database.
+
+To reproduce a source import, use `registry.build(name, source_paths=...)`,
+`orfdata datasets build NAME`, or `orfdata.sources.pfizer.build_protein("dog")`.
+The source overrides are `protein.tsv` and `search.fasta`; DataCache verifies
+their original checksums before running the importer. Source slices with actual
+positive, zero and missing values test the same importer for all three species.