orfdata 0.42.2__tar.gz → 0.42.3__tar.gz

{orfdata-0.42.2 → orfdata-0.42.3}/MANIFEST.in

@@ -15,3 +15,4 @@ recursive-include tests/data/ncorf_mammals *.bed *.fa *.xlsx *.gz *.md
 recursive-include tests/data/riborf *.xlsx *.gz *.md
 recursive-include tests/data/kaabinejadian *.zip *.tsv
 recursive-include tests/data/peptideatlas *.zip *.gz
+recursive-include tests/data/mammary_stroma *.gz *.txt *.xml

{orfdata-0.42.2/orfdata.egg-info → orfdata-0.42.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.42.2
+Version: 0.42.3
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0

{orfdata-0.42.2 → orfdata-0.42.3}/docs/coverage.md

@@ -8,13 +8,14 @@ data coverage, independently of what the API can represent.
 | --- | --- | --- | --- |
 | Human | Wang: 29 specimens, gene/transcript FPKM and estimated copies/cell | Wang: 15,210 groups, iBAQ and estimated copies/cell; Pfizer: 10,352 groups, 37 channels, iBAQ/rIBAQ | Wang: adjacent cryosections; Pfizer: native RNA missing |
 | Mouse | Pfizer: 606 libraries, 56,051 gene targets, counts | Pfizer: 12,124 groups, 63 channels, iBAQ/rIBAQ | Unresolved library-to-pool correspondence |
-| Dog | Pfizer: 434 libraries, 30,941 gene targets, counts | Pfizer: 9,929 groups, 38 channels, iBAQ/rIBAQ | Unresolved library-to-pool correspondence |
+| Dog | Pfizer: 434 libraries, 30,941 gene targets, counts; mammary stroma: 18,582 genes × 30 samples | Pfizer: 9,929 groups, 38 channels, iBAQ/rIBAQ; mammary stroma: 1,583 native groups × 28 samples | Mammary stroma: 14 shared specimens, 28 paired compartments and two RNA samples without protein mates; Pfizer crosswalk remains unresolved |
 | Budding yeast | CoPY: four RNA libraries plus a source aggregate, FPKM and estimated copies/cell; Ingolia: four RNA libraries, counts and densities | CoPY: calibrated SRM and separately calibrated label-free estimates | CoPY: explicit source-cohort pairing; individual cross-assay replicate matches unknown |
 
 ## Peptides and MHC ligands
 
-Dog has three peptide-level datasets:
+Dog has four peptide-level datasets:
 
+- **Mammary stroma** ([guide](mammary-stroma.md)): 5,413 native peptide rows, intensity and LFQ columns, reported group memberships and original control/decoy flags across 28 samples.
 - **Pfizer native peptide evidence** ([guide](pfizer-peptides.md)): 953,980 target
   peptide sequences, native peptide/PSM reporter quantities and reported protein-group
   memberships. The 96 runs retain 38 tissue pools, four bridge channels and two
@@ -28,7 +29,7 @@ Dog has three peptide-level datasets:
   dog tumours, each searched against four protein databases, and from three
   human HCT 116 lines that each express one DLA-88 allele.
 
-All three searched known proteins only. Other species have no peptide-level
+All four searched known proteins only. Other species have no peptide-level
 measurement dataset yet; the human and mouse ORF catalogues carry pooled
 peptide evidence for their noncanonical ORFs.
 

{orfdata-0.42.2 → orfdata-0.42.3}/docs/dog-data-sources.md

@@ -1,7 +1,8 @@
 # Canine paired measurements and translation-evidence audit
 
 Source check: **28 October 2026**. This audit identifies importable measurement
-files and their limitations. It does not add a dataset to the registry.
+files and their limitations. The subsequent [mammary-stroma importer](mammary-stroma.md)
+now exposes the paired study through the common quantitative registry.
 The [machine-readable audit](data/dog-source-audit-20261028.json) contains source
 URLs, hashes, counts, search queries and a candidate sample crosswalk.
 
@@ -37,7 +38,8 @@ deposited search used a dated canonical UniProt reference, but its FASTA is not
 among the 31 PRIDE files. Sequence/reference qualification remains necessary;
 these data do not establish ncORF translation. Author-derived contrasts in the
 supplementary workbooks must stay distinct from sample-level measurements.
-Import work remains tracked in [#20](https://github.com/openvax/orfdata/issues/20).
+The paired study is now imported as `canine-mammary-stroma`; the remaining dog
+data requests stay tracked in [#20](https://github.com/openvax/orfdata/issues/20).
 
 ## Dog Ribo-seq and ncORF translation
 

orfdata-0.42.3/docs/mammary-stroma.md

@@ -0,0 +1,104 @@
+# Paired canine mammary-stroma RNA and protein
+
+`canine-mammary-stroma` imports the processed measurements of
+[Amini et al. (2021)](https://doi.org/10.1016/j.neo.2021.03.001),
+[GSE135183](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135183) and
+[PXD023023](https://www.ebi.ac.uk/pride/archive/projects/PXD023023).
+It uses the same data commands and `QuantitativeDataset` API as other species
+and sources:
+
+```sh
+orfdata data info canine-mammary-stroma
+orfdata data fetch canine-mammary-stroma
+orfdata data path canine-mammary-stroma
+```
+
+```python
+from orfdata import DatasetRegistry
+
+registry = DatasetRegistry()
+dataset = registry.open("canine-mammary-stroma")  # Offline; no implicit download.
+rna_reference, protein_reference = dataset.manifest.references
+pairs = list(dataset.pairings())
+complete_pairs = [pair for pair in pairs if pair.right_assay_id is not None]
+pair = complete_pairs[0]
+rna = dataset.measurements(
+    reference=pair.reference, assay_id=pair.left_assay_id, unit="estimated_count"
+)
+protein = dataset.measurements(
+    reference=pair.right_reference, assay_id=pair.right_assay_id, unit="LFQ intensity"
+)
+```
+
+The release contains 993,560 native measurements in a 52 MB download and a
+514 MB installed SQLite file. Rebuilding uses approximately 8 MB of pinned processed inputs; no raw MS
+files, sequencing reads, alignment index or vendor database is required.
+
+| Layer | Native scope | Quantities |
+| --- | --- | --- |
+| RNA | 18,582 Ensembl gene IDs × 30 samples, 15 cases | Integer estimated counts from Kallisto/tximport |
+| Protein | 1,583 native MaxQuant groups × 28 samples, 14 cases | Intensity, LFQ intensity, iBAQ |
+| Peptide | 5,413 native peptide rows × 28 samples | Intensity and the separately reported LFQ intensity columns |
+
+Different quantitative columns do not add biological replicates. The 58
+assays retain their original sample and run identities. Native MS rows include
+77 reversed protein groups and 52 contaminant groups; these counts are not
+counts of confidently detected canine proteins.
+
+## Specimen pairing
+
+The authors reused archived FFPE mammary specimens for separate laser-capture
+RNA and protein preparations. The importer verifies a unique match between
+clinical Table 1 and GEO by breed, age and histological subtype, recording
+spelling normalizations and both original sets of labels. This is a
+**metadata-derived crosswalk within an author-declared shared cohort**, not an
+author-provided case-ID mapping.
+
+Fourteen shared cases give 28 complete assay pairs: normal stroma and
+cancer-associated stroma separately. Two RNA samples from GEO case 127 have
+explicitly missing protein mates; the paper reports exclusion of proteomics
+case 7 because its paraffin block was unavailable. No protein sample is invented.
+
+These pairs use `same_specimen`. This basis means separate preparations from the
+same original specimen, without claiming identical aliquots or adjacent
+sections. Temporal labels refer to the original biological specimen, not the
+dates of RNA sequencing and mass-spectrometry acquisition. Missing mates retain
+an unknown temporal relationship. Pairing does not itself establish a
+relationship between RNA genes and protein groups: this release has no
+cross-modal target relations or current-reference mappings.
+
+The normal compartment belongs to a cancer-bearing mammary specimen. It is not
+a healthy-animal normal-tissue atlas. Source case IDs identify individual
+specimens, and repeated compartments or quantities never imply additional dogs.
+
+## Missingness, native records and reference limits
+
+- RNA zeros remain measured zero counts. Counts are estimated gene-level values,
+  with no conversion to TPM, copies per cell or translation efficiency.
+- MaxQuant MS zeros denote unquantified cells. Their numeric values are `None`
+  with status `missing`; the original `"0"` survives in provenance. The 2,156
+  native `"NaN"` iBAQ cells also remain missing, with a separate reason.
+- Every native MS field survives once in the corresponding mapping's
+  `provenance["native_record"]`. Measurements retain source row/column, original
+  numeric text, identification type and the original control/decoy flags.
+- Peptide mappings retain every reported native protein-group ID. A unique
+  assignment to one *group* is not unique protein or isoform detection. Group
+  records retain reported protein labels, including contaminants, without
+  assigning them to a canine biological protein reference.
+- No source QC threshold, aggregation, imputation, differential-expression model
+  or RNA/protein ratio is applied. Consumers can inspect the native flags and
+  scores explicitly.
+
+RNA was quantified against Ensembl transcripts on CanFam3.1; its exact release
+and transcript sequence bytes are not reported. The protein search used a
+canonical UniProt dog reference dated 2019-07-29 with decoys and contaminants;
+the searched FASTA is absent from the deposited processed files. Both references
+remain source-bound and incomplete. Source membership and uniqueness flags are
+preserved, but no full-background sequence uniqueness is asserted. These data
+provide neither ncORF translation evidence nor MHC-presentation evidence.
+
+The [earlier source audit](dog-data-sources.md) records the acquisition and
+crosswalk evidence. The PRIDE project declares CC0; GEO numerical data and
+factual metadata use [GEO's public-data terms](https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html).
+Factual clinical curation cites Table 1 of the CC BY-NC-ND article. Its original
+text and figures are excluded from the dataset artifact.

{orfdata-0.42.2 → orfdata-0.42.3}/docs/pairing.md

@@ -17,7 +17,7 @@ a Cartesian product of technical replicates. Each row retains its assay pairing
 and target relationship. A three-assay experiment can declare several pairwise
 comparisons; sharing an RNA measurement does not create independent replicates.
 
-Pairing bases are `same_material`, `adjacent_donor_tissue`,
+Pairing bases are `same_material`, `same_specimen`, `adjacent_donor_tissue`,
 `biological_replicate`, `independent_cultures`, `tissue_aggregate` and
 `condition_aggregate`. The caller must choose the allowed bases. By default,
 only explicitly concurrent assays are returned; opt into `longitudinal` or
@@ -116,3 +116,8 @@ identities nor transfers abundance or protein-existence evidence. ORF comparison
 additionally require their own sequence, frame and positional evidence and
 `allow_orfs=True`; a gene ortholog cannot establish an orthologous ncORF.
 Human, mouse, dog, yeast and arbitrary other taxa use this same API.
+
+`same_specimen` records separate preparations from the same original specimen.
+It does not assert identical aliquots (`same_material`) or adjacent sections.
+The [canine mammary-stroma dataset](mammary-stroma.md) uses this distinction and
+retains missing mates explicitly.

{orfdata-0.42.2 → orfdata-0.42.3}/mkdocs.yml

@@ -41,6 +41,7 @@ nav:
       - Human, mouse and dog protein: pfizer-protein.md
       - Pfizer dog peptide and group evidence: pfizer-peptides.md
       - Dog and mouse RNA: pfizer-rna.md
+      - Paired canine mammary stroma: mammary-stroma.md
       - Yeast protein and RNA: copy-yeast.md
       - Yeast RNA and ribosome occupancy: ingolia-yeast.md
       - Dog MHC ligands and PeptideAtlas: dog-peptides.md

{orfdata-0.42.2 → orfdata-0.42.3}/orfdata/data/datasets.json

@@ -3283,5 +3283,260 @@
         }
       }
     }
+  },
+  "canine-mammary-stroma": {
+    "default_version": "2026-10-29.1",
+    "versions": {
+      "2026-10-29.1": {
+        "manifest": {
+          "dataset_id": "canine-mammary-stroma",
+          "version": "2026-10-29.1",
+          "title": "Canine paired mammary-stroma RNA and native protein/peptide measurements",
+          "references": [
+            {
+              "taxon_id": 9615,
+              "species": "dog",
+              "genome_build": "CanFam3.1",
+              "annotation_name": "ensembl",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": null,
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": "a199bafcc51fefdd3a4231710d0ad6b157a3f9d6c25ae42c26b0bac0c44667c2"
+            },
+            {
+              "taxon_id": 9615,
+              "species": "dog",
+              "genome_build": null,
+              "annotation_name": "uniprot",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": null,
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": "67360353510fdb77cc970f671ca9ec17b07686f2dc5771bb6804d182d5c17423"
+            }
+          ],
+          "sources": [
+            {
+              "asset_id": "proteinGroups.txt",
+              "url": "https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/proteinGroups.txt",
+              "sha256": "67360353510fdb77cc970f671ca9ec17b07686f2dc5771bb6804d182d5c17423",
+              "size": 2784425,
+              "access_terms": "PRIDE dataset PXD023023: Creative Commons Public Domain CC0, as declared by project API. Attribution: Amini et al.",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "proteinGroups.txt",
+                "terms_verified": "2026-10-29"
+              }
+            },
+            {
+              "asset_id": "peptides.txt",
+              "url": "https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/peptides.txt",
+              "sha256": "8964af6adbe8ac6fce6897f5eeaaf5da3d7c72fe2eb78ee2653901876a2f0172",
+              "size": 4492377,
+              "access_terms": "PRIDE dataset PXD023023: Creative Commons Public Domain CC0, as declared by project API. Attribution: Amini et al.",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "peptides.txt",
+                "terms_verified": "2026-10-29"
+              }
+            },
+            {
+              "asset_id": "rna.csv.gz",
+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135183/suppl/GSE135183_raw_counts.csv.gz",
+              "sha256": "de3fc2a57fa05682996b328929c94fc51eadd126ec2299870b8f46b24be46a67",
+              "size": 605819,
+              "access_terms": "Public GEO deposited numerical data and factual metadata; NCBI imposes no use/distribution restrictions. Attribution: Amini et al., GSE135183.",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "GSE135183_raw_counts.csv.gz",
+                "terms_verified": "2026-10-29"
+              }
+            },
+            {
+              "asset_id": "geo.soft.gz",
+              "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135183/soft/GSE135183_family.soft.gz",
+              "sha256": "a199bafcc51fefdd3a4231710d0ad6b157a3f9d6c25ae42c26b0bac0c44667c2",
+              "size": 4022,
+              "access_terms": "Public GEO deposited numerical data and factual metadata; NCBI imposes no use/distribution restrictions. Attribution: Amini et al., GSE135183.",
+              "license_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "GSE135183_family.soft.gz",
+                "terms_verified": "2026-10-29"
+              }
+            },
+            {
+              "asset_id": "paper.xml",
+              "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8042244/fullTextXML",
+              "sha256": "c933efb05e263a4d6106c93b2e5344f9ecec08e7875633ec38eef069dfad171a",
+              "size": 156278,
+              "access_terms": "CC BY-NC-ND 4.0 article; acquired locally to validate factual Table 1. Original article text and figures excluded from generated artifacts.",
+              "license_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
+              "redistributable": false,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "PMC8042244.xml",
+                "terms_verified": "2026-10-29"
+              }
+            },
+            {
+              "asset_id": "project.json",
+              "url": "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD023023",
+              "sha256": "75271e3cdfb38c259509ed9564268564d5c7aababb4c602efa74076e0831668d",
+              "size": 9687,
+              "access_terms": "PRIDE dataset PXD023023: Creative Commons Public Domain CC0, as declared by project API. Attribution: Amini et al.",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Amini et al.; University of Zurich",
+                "source_filename": "PXD023023.json",
+                "terms_verified": "2026-10-29"
+              }
+            }
+          ],
+          "citations": [
+            "https://doi.org/10.1016/j.neo.2021.03.001",
+            "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135183",
+            "https://www.ebi.ac.uk/pride/archive/projects/PXD023023"
+          ],
+          "assay_kinds": [
+            "rna_seq",
+            "digest_ms"
+          ],
+          "coverage": {
+            "accessions": [
+              "GSE135183",
+              "PXD023023"
+            ],
+            "rna_genes": 18582,
+            "rna_samples": 30,
+            "protein_samples": 28,
+            "shared_specimens": 14,
+            "paired_compartments": 28,
+            "rna_without_protein": 2,
+            "tables": {
+              "proteinGroups.txt": {
+                "header_sha256": "8f5e81ad809c172f2e4bb7cec1a8a6cdb1c427e232cf0bc7a0434b5e7df4b1ef",
+                "rows": 1583,
+                "measurement_statuses": {
+                  "intensity:measured": 19910,
+                  "intensity:missing": 24414,
+                  "LFQ intensity:missing": 36303,
+                  "LFQ intensity:measured": 8021,
+                  "iBAQ:measured": 18951,
+                  "iBAQ:missing": 25373
+                },
+                "qc_counts": {
+                  "Reverse": {
+                    "": 1506,
+                    "+": 77
+                  },
+                  "Potential contaminant": {
+                    "+": 52,
+                    "": 1531
+                  }
+                }
+              },
+              "peptides.txt": {
+                "header_sha256": "b5ee266d1d5ae348f902e2332e94bef7cec49d90978bba16370247767481b5eb",
+                "rows": 5413,
+                "measurement_statuses": {
+                  "intensity:missing": 92422,
+                  "intensity:measured": 59142,
+                  "LFQ intensity:missing": 92422,
+                  "LFQ intensity:measured": 59142
+                },
+                "qc_counts": {
+                  "Reverse": {
+                    "": 5336,
+                    "+": 77
+                  },
+                  "Potential contaminant": {
+                    "": 4997,
+                    "+": 416
+                  }
+                }
+              }
+            },
+            "normal_tissue_scope": "Normal stromal compartments of cancer-bearing specimens, not healthy-dog baseline tissue",
+            "reference_limits": "RNA Ensembl release unspecified. Protein canonical UniProt search date 2019-07-29; exact FASTA unavailable. No current-reference or gene/protein identity projection.",
+            "measurement_limits": "Native estimated counts and MS intensities; no copies/cell, imputation, RNA/protein ratios or isoform allocation.",
+            "qc_scope": "All native rows retained, including contaminants and reversed decoys, with source QC flags. No implicit acceptance threshold.",
+            "translation_scope": "Bulk digest proteomics; no ncORF search or translation evidence and no MHC presentation evidence",
+            "pairing_limits": "Metadata-derived case crosswalk within author-declared shared FFPE cohort; separate preparations, no same-aliquot or adjacent-section assertion."
+          },
+          "processing": {
+            "software": "orfdata",
+            "version": "0.42.3",
+            "importer": "canine-mammary-stroma-v1",
+            "specimen_crosswalk": {
+              "1": "135",
+              "2": "134",
+              "3": "121",
+              "4": "123",
+              "5": "126",
+              "6": "109",
+              "8": "128",
+              "9": "131",
+              "10": "130",
+              "11": "132",
+              "12": "138",
+              "13": "139",
+              "14": "136",
+              "15": "137"
+            },
+            "operations": [
+              "Validate native samples and source bytes",
+              "Reconcile unique case metadata with explicit source spelling aliases",
+              "Retain reported quantitative scales and all native MS row fields",
+              "Treat zero MS intensity as unquantified; retain native zero text",
+              "Keep RNA zeros measured",
+              "Declare same-specimen assay pairs and missing mates without gene/protein inference"
+            ],
+            "parameters": {
+              "aggregate_replicates": false,
+              "impute_missing": false,
+              "allocate_group_abundance": false
+            },
+            "specimen_identity_aliases": {
+              "Bassett": "Basset",
+              "Viszla": "Vizsla",
+              "n.d.": "not disclosed",
+              "tubulo-papillary": "tubulopapillary"
+            },
+            "source_note": "Paper Table 1 and GEO case numbers differ; crosswalk derived from unique breed/age/histology within the explicitly shared cohort. Protein case 7 was excluded; RNA 127 has no matching proteomics specimen."
+          },
+          "schema": "orfdata.measurements.v1"
+        },
+        "assets": {
+          "dataset.sqlite": {
+            "url": "https://github.com/openvax/orfdata/releases/download/data-canine-mammary-stroma-2026-10-29.1/canine-mammary-stroma-2026-10-29.1.sqlite.gz",
+            "decompress": true,
+            "size": 514154496,
+            "sha256": "98301b7ff5c7fb71640491de65de7631db5dfa3288e3b0ecb2ec2c8ebd721ef2"
+          }
+        },
+        "distribution": {
+          "redistributable": true,
+          "access_terms": "PRIDE CC0 quantitative facts; public GEO numerical data and factual metadata under GEO terms; factual clinical curation with citation to the CC BY-NC-ND article, whose text/figures are excluded. ORFdata code Apache-2.0.",
+          "data_release": "data-canine-mammary-stroma-2026-10-29.1",
+          "download_size": 52014803,
+          "download_sha256": "0afcff9d3b8e23c9cd3fbb91f93f13095e9cec20b478e1f837afba71c202b90a",
+          "installed_size": 514154496
+        }
+      }
+    }
   }
 }

{orfdata-0.42.2 → orfdata-0.42.3}/orfdata/pairing.py

@@ -16,7 +16,7 @@ from .measurements import (
 from .reference import ReferenceContext, ScopedTarget
 
 PAIRING_BASES = (
-    "same_material", "adjacent_donor_tissue", "biological_replicate",
+    "same_material", "same_specimen", "adjacent_donor_tissue", "biological_replicate",
     "independent_cultures", "tissue_aggregate", "condition_aggregate",
 )
 TEMPORAL_RELATIONS = ("concurrent", "longitudinal", "unknown")

{orfdata-0.42.2 → orfdata-0.42.3}/orfdata/sources/__init__.py

@@ -3,6 +3,10 @@
 
 def importer(name):
     """Resolve a packaged importer, never execute an import path from metadata."""
+    if name == "canine-mammary-stroma-v1":
+        from .mammary_stroma import import_stroma
+
+        return import_stroma
     if name == "pfizer-protein-v1":
         from .pfizer import import_protein