orfdata 0.31.0__tar.gz → 0.32.0__tar.gz

{orfdata-0.31.0 → orfdata-0.32.0}/MANIFEST.in

@@ -12,3 +12,5 @@ recursive-include tests/data/ingolia *.gz *.txt
 recursive-include tests/data/openprot *.zip *.gz
 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

{orfdata-0.31.0/orfdata.egg-info → orfdata-0.32.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.31.0
+Version: 0.32.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -139,6 +139,7 @@ orfdata datasets download ingolia-yeast-rna-ribo
 | [Matched human tissues](https://openvax.github.io/orfdata/human-tissue/) | Human | RNA and protein from adjacent cryosections (Wang et al.) |
 | [Yeast protein and RNA](https://openvax.github.io/orfdata/copy-yeast/) | Budding yeast | Calibrated protein and RNA abundance (CoPY) |
 | [Yeast RNA and ribosome occupancy](https://openvax.github.io/orfdata/ingolia-yeast/) | Budding yeast | Source regions, including UTR and ncRNA labels (Ingolia et al.) |
+| [Dog peptides](https://openvax.github.io/orfdata/dog-peptides/) | Dog | DLA class I ligands from tumours (Kaabinejadian et al.); Canine PeptideAtlas peptides and protein calls, built locally |
 
 Gene RNA and canonical protein measurements do not establish noncanonical ORF
 abundance. See [released data and gaps](https://openvax.github.io/orfdata/coverage/).

{orfdata-0.31.0 → orfdata-0.32.0}/README.md

@@ -107,6 +107,7 @@ orfdata datasets download ingolia-yeast-rna-ribo
 | [Matched human tissues](https://openvax.github.io/orfdata/human-tissue/) | Human | RNA and protein from adjacent cryosections (Wang et al.) |
 | [Yeast protein and RNA](https://openvax.github.io/orfdata/copy-yeast/) | Budding yeast | Calibrated protein and RNA abundance (CoPY) |
 | [Yeast RNA and ribosome occupancy](https://openvax.github.io/orfdata/ingolia-yeast/) | Budding yeast | Source regions, including UTR and ncRNA labels (Ingolia et al.) |
+| [Dog peptides](https://openvax.github.io/orfdata/dog-peptides/) | Dog | DLA class I ligands from tumours (Kaabinejadian et al.); Canine PeptideAtlas peptides and protein calls, built locally |
 
 Gene RNA and canonical protein measurements do not establish noncanonical ORF
 abundance. See [released data and gaps](https://openvax.github.io/orfdata/coverage/).

{orfdata-0.31.0 → orfdata-0.32.0}/docs/catalogs.md

@@ -341,15 +341,16 @@ No public resource gives dog ORF-level translation evidence, as of October
   rough-ER microsomes), deposited no reads.
 - **Mass spectrometry.** Every dog dataset searched canonical proteins only,
   so none reports a noncanonical peptide as deposited: the Canine
-  PeptideAtlas (PXD052932, 245,884 peptides from 13 tissues, plasma and
-  urine), the dog tumour DLA immunopeptidome (PXD074485, about 12,700
-  ligands), the Pfizer TMT atlas (PXD070290) and the dog brain proteome
-  (PXD033420, PXD034449).
+  PeptideAtlas (PXD052932, 149,546 peptides from 13 tissues, plasma and
+  urine), the dog tumour DLA immunopeptidome (PXD074485, 12,949 distinct
+  database-search ligands), the Pfizer TMT atlas (PXD070290) and the dog brain
+  proteome (PXD033420, PXD034449). The first two are available as
+  [dog peptide datasets](dog-peptides.md), as evidence for known proteins.
 
 Dog ncORF evidence therefore needs those spectra searched again against dog
 ORF sequences. Human and mouse ORFs are never transferred to dog by orthology.
-Dog proteomes contain their PyEnsembl-annotated proteins, and dog RNA and
-protein abundance are available as [measurements](measurements.md).
+Dog proteomes contain their PyEnsembl-annotated proteins, and dog RNA, protein
+abundance and peptides are available as [measurements](measurements.md).
 
 ## Every assembly of a species
 

{orfdata-0.31.0 → orfdata-0.32.0}/docs/coverage.md

@@ -11,6 +11,23 @@ data coverage, independently of what the API can represent.
 | Dog | Pfizer: 434 libraries, 30,941 gene targets, counts | Pfizer: 9,929 groups, 38 channels, iBAQ/rIBAQ | Unresolved library-to-pool correspondence |
 | 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 two peptide-level datasets ([guide](dog-peptides.md)):
+
+- **Canine PeptideAtlas** (build 573): 149,546 tryptic peptides with PSM counts
+  in 18 Labrador tissue, plasma and urine samples, every protein location, and
+  17,795 protein calls, 17,110 of them mapped to Ensembl 110 proteins with an
+  identical sequence. PeptideAtlas states no licence,
+  so this dataset is built locally from its download and never redistributed.
+- **DLA class I ligands** (Kaabinejadian et al.): 76,550 PEAKS rows from four
+  dog tumours, each searched against four protein databases, and from three
+  human HCT 116 lines that each express one DLA-88 allele.
+
+Both 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.
+
 ## Reading the table
 
 - Gene targets include measured zeros; their presence in a matrix does not imply

orfdata-0.32.0/docs/dog-peptides.md

@@ -0,0 +1,147 @@
+# Dog peptides: MHC ligands and the Canine PeptideAtlas
+
+Two dog peptide datasets record which peptides of known dog proteins mass
+spectrometry has observed. Neither searched for noncanonical ORFs, so they
+don't add ORFs to the dog proteome
+([why dog has no ncORF catalogue](catalogs.md#dog)).
+
+| Dataset | What it holds | How to get it |
+|---|---|---|
+| `kaabinejadian-dog-dla-ligands` | DLA class I ligands from four dog tumours and three DLA-88 monoallelic cell lines | `orfdata datasets download` (CC0, 25 MB) |
+| `peptideatlas-dog-peptides` | 149,546 tryptic peptides from 18 Labrador tissue, plasma and urine samples, with genome locations | `orfdata datasets build` (built locally from 71 MB of sources) |
+
+## DLA class I ligands
+
+[Kaabinejadian et al. (2026)](https://doi.org/10.1016/j.isci.2026.115975)
+eluted peptides from DLA class I molecules with the BB7.6 or H58A antibody. PRIDE
+[PXD074485](https://www.ebi.ac.uk/pride/archive/projects/PXD074485) deposits
+their PEAKS Studio 11.5 peptide tables (1% FDR), which this dataset imports in
+full: 76,550 rows, each with its PEAKS area, intensity and spectrum count.
+
+| Sample | Tumour | Breed | DLA-88 typing | Antibodies |
+|---|---|---|---|---|
+| Lola | osteosarcoma | Black Russian Terrier | \*501:01 | BB7.6, H58A |
+| 163828A | anal sac adenocarcinoma | English Cocker Spaniel | \*004:02 | BB7.6 |
+| Lily | anal sac adenocarcinoma | English Cocker Spaniel | \*501:01, \*501:02, \*004:02 | H58A |
+| Bogey | oral melanoma | American Cocker Spaniel | \*003:02, \*006:01, \*017:01 | BB7.6 |
+| HCT116-DLA88… | human HCT 116 cells, one DLA-88 allele each | — | \*003:02, \*012:01 or \*501:01 | BB7.6 |
+
+Each tumour's spectra were searched four times: against UniProt's dog
+proteome, Basenji and Great Dane (Zoey) Ensembl 104 proteins, and a merged
+database of four dog assemblies. Each search is its own assay
+(`Lola-BB76:UniProt9615`, `Lola-BB76:MergedCanFams`, ...). A peptide found in
+two searches of one sample is one observation, not two. The HCT 116 lines were
+searched against human SwissProt, and their peptides are human proteins, so
+they sit in the dataset's separate human reference context.
+
+Database search finds 11,363 distinct dog peptides in the UniProt searches and
+12,949 across all four databases. For the cell lines, the counts of unique
+8–14-mers from database search (591 for DLA-88\*003:02, 1,465 for \*501:01) match
+the article's. The article's tumour counts come from its curated supplementary
+lists, which aren't imported (they are CC BY-NC-ND), and match no single table.
+
+Every row keeps its PEAKS identification type in provenance as `found_by`:
+`DB Search`, `DeepNovo` (de novo sequencing) or `Homolog` (SPIDER homology
+search). Only database-search peptides are guaranteed to occur in a listed
+protein, so filter on it for a conservative ligand list. Rows of the Biognosys
+iRT retention-time standards and their fragments (2,242) are marked
+`irt_standard` in every search. That includes the merged database, which lacks
+the kit, so PEAKS named dog proteins for them there.
+
+```python
+from orfdata import DatasetRegistry, ScopedTarget
+
+registry = DatasetRegistry()
+ligands = registry.open("kaabinejadian-dog-dla-ligands")  # After downloading it.
+dog = next(r for r in ligands.manifest.references if r.taxon_id == 9615)
+
+# Where a peptide was eluted, and how it was identified.
+peptide = ScopedTarget(dog, "peptide", "AIKKGLEEL", "amino-acid-sequence")
+for m in ligands.measurements(target=peptide, quantity="spectrum_count"):
+    print(m.sample_id, m.assay_id, m.value, m.provenance["found_by"])
+
+# Lola's database-search ligands (BB7.6, UniProt search).
+lola = {m.target.identifier for m in ligands.measurements(
+            reference=dog, assay_id="Lola-BB76:UniProt9615", quantity="spectrum_count")
+        if m.provenance["found_by"] == "DB Search" and not m.provenance["irt_standard"]}
+```
+
+Targets are unmodified sequences; each row's modified form (for example
+`M(+15.99)`) is in its provenance as `peptide`. `mappings()` lists, for each
+search and identification type, the proteins PEAKS reported for a peptide:
+`unique` or `ambiguous` for database-search and homology matches, and
+`unmapped` with a reason for iRT standards and de novo sequences, whose listed
+proteins stay in the mapping's evidence. The search FASTAs weren't deposited,
+so no accession can be checked against a sequence.
+
+Each row also records `raw_file_deposited`. For 1,695 rows the best spectrum
+comes from a run missing from the deposit: Lily's second injection (22-1107,
+299 rows) and the first DLA-88\*012:01 runs (20240929, 1,396 rows). The raw
+files of 163828A's H58A run have no deposited results and aren't included.
+
+## Canine PeptideAtlas
+
+The [Canine PeptideAtlas](https://peptideatlas.org/builds/canine/)
+([Kusebauch et al. 2026](https://doi.org/10.1038/s41597-026-06647-z))
+reprocessed 138 runs from Labrador Retrievers (13 tissues, plasma and urine;
+PRIDE PXD052932) at a PSM FDR of 0.001. This dataset imports its 2024-01 build
+(573):
+
+- PSM counts for 149,546 peptides in each of the 18 samples where they were
+  observed (528,272 values);
+- every protein each peptide maps to, with its position and, for Ensembl
+  proteins, its ROS_Cfam_1.0 coordinates (exon-spanning peptides have one
+  location per exon);
+- the build's 17,795 protein calls with presence levels (6,423 canonical). Of
+  its 17,307 UniProt and Ensembl calls, 16,959 map to one Ensembl 110 protein
+  with an identical sequence, 151 to several and 197 to none; contaminant and
+  decoy calls aren't mapped.
+
+PeptideAtlas states no licence for its downloads, so orfdata never
+redistributes this dataset. `build` downloads the build's 61 MB export and
+Ensembl 110's dog proteins, checks their SHA-256, and builds the dataset
+locally (about a minute; 540 MB on disk). After that, `open` works offline.
+
+```sh
+orfdata datasets build peptideatlas-dog-peptides
+```
+
+```python
+from pyensembl import EnsemblRelease
+from orfdata import DatasetRegistry, ScopedTarget
+
+atlas = DatasetRegistry().open("peptideatlas-dog-peptides")  # After building it.
+source, ensembl = atlas.manifest.references
+
+# PSMs of one peptide in each sample.
+peptide = ScopedTarget(source, "peptide", "AAHEEICTTNEGVMYR", "amino-acid-sequence")
+for m in atlas.measurements(target=peptide):
+    print(m.sample_id, m.value)
+
+# The PeptideAtlas call for a PyEnsembl dog protein (albumin).
+transcript = EnsemblRelease(110, species="dog").transcript_by_id("ENSCAFT00845010439")
+protein = ScopedTarget(ensembl, "protein", transcript.protein_id, "ensembl")
+for mapped in atlas.mapped_measurements(protein, require_sequence=True):
+    call = mapped.measurement
+    print(call.target.identifier, call.value, call.provenance["presence_level"])
+```
+
+The `ensembl` context is exactly PyEnsembl's dog release 110
+(`ReferenceContext.from_genome(EnsemblRelease(110, species="dog"))`), so
+PyEnsembl protein IDs work directly. The [dog RNA dataset](pfizer-rna.md) uses
+Ensembl 110 IDs too, in a context that also pins its GTF. Ensembl 105–111 have
+identical sequences for all 25,710 Ensembl proteins in PeptideAtlas's search
+set.
+
+Each peptide's mapping (`mappings()`, keyed by PeptideAtlas accession) keeps its
+locations as `[protein, start, end, chromosome, strand, chromosome_start,
+chromosome_end, exact]`. `exact` is false for the 4,767 locations where the
+protein has isoleucine for leucine or the reverse, which PeptideAtlas maps as
+equal. 204 peptides map only to decoy sequences; they pass the FDR threshold but
+are probably false identifications, and are `unmapped` with that reason.
+
+A protein call's PSM count includes peptides it shares with other proteins, so
+calls don't add up to the build's 13,781,115 PSMs. PeptideAtlas's web page
+reports 245,884 peptides and 13,716,253 PSMs for the build; its export, which
+this dataset reproduces, has 149,546 peptides (197,285 distinct modified forms)
+and 13,781,115 PSMs.

{orfdata-0.31.0 → orfdata-0.32.0}/docs/measurements.md

@@ -13,6 +13,7 @@ Released datasets, each with its own guide:
 - [Matched human tissue RNA and protein](human-tissue.md) (Wang et al.)
 - [Yeast protein and RNA abundance](copy-yeast.md) (CoPY)
 - [Yeast RNA and ribosome occupancy](ingolia-yeast.md) (Ingolia et al.)
+- [Dog MHC ligands and PeptideAtlas peptides](dog-peptides.md) (Kaabinejadian et al.; Kusebauch et al.)
 
 See [released coverage and gaps](coverage.md); the
 [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks further

{orfdata-0.31.0 → orfdata-0.32.0}/docs/storage.md

@@ -13,7 +13,13 @@ Zeros, nulls, censoring, uncertainty, nested provenance and derived inputs retai
 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
+ORFdata 0.32 writes storage version 5, which also stores each target mapping's
+candidates as kind, identifier and namespace: they always share the mapping's
+reference, which its row already names. The dog DLA ligand dataset, with 62,492
+mappings, is 255 MB, against 389 MB in the version 4 layout. Version 4 files remain readable, and a
+version 4 fixture written by the released ORFdata 0.30.0 tests that.
+
+Published storage versions 1, 2, 3 and 4 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

{orfdata-0.31.0 → orfdata-0.32.0}/mkdocs.yml

@@ -40,6 +40,7 @@ nav:
       - Dog and mouse RNA: pfizer-rna.md
       - Yeast protein and RNA: copy-yeast.md
       - Yeast RNA and ribosome occupancy: ingolia-yeast.md
+      - Dog MHC ligands and PeptideAtlas: dog-peptides.md
   - Project:
       - Release notes: https://github.com/openvax/orfdata/blob/main/CHANGELOG.md
       - Data roadmap: https://github.com/openvax/orfdata/issues/3