orfdata 0.5.0__tar.gz → 0.6.0__tar.gz

{orfdata-0.5.0 → orfdata-0.6.0}/MANIFEST.in

@@ -1,3 +1,3 @@
 include lint.sh test.sh deploy.sh
 recursive-include docs *.md
-recursive-include tests *.py *.json *.md
+recursive-include tests *.py *.json *.md *.tsv *.fasta

{orfdata-0.5.0/orfdata.egg-info → orfdata-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.5.0
+Version: 0.6.0
 Summary: Reference open reading frames and experimental translation evidence on annotated transcripts
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -95,12 +95,16 @@ 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) uses the same
+species-scoped API. These canonical-search protein groups 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 RNA abundance, ribosome occupancy, yeast absolute quantification and
+additional protein data releases.

{orfdata-0.5.0 → orfdata-0.6.0}/README.md

@@ -68,12 +68,16 @@ 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) uses the same
+species-scoped API. These canonical-search protein groups 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 RNA abundance, ribosome occupancy, yeast absolute quantification and
+additional protein data releases.

{orfdata-0.5.0 → orfdata-0.6.0}/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-0.6.0/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.

orfdata-0.6.0/orfdata/data/datasets.json

@@ -0,0 +1,388 @@
+{
+  "pfizer-atlas-human-protein": {
+    "default_version": "2026-10-12.1",
+    "versions": {
+      "2026-10-12.1": {
+        "manifest": {
+          "dataset_id": "pfizer-atlas-human-protein",
+          "version": "2026-10-12.1",
+          "title": "Pfizer/Oziolor human native protein-group abundance",
+          "references": [
+            {
+              "taxon_id": 9606,
+              "species": "human",
+              "genome_build": null,
+              "annotation_name": "uniprot",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": "3793b9bfcc956a278494734bb775a010513f5764d8047fcdb283d2aeaa7fefb8",
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": null
+            }
+          ],
+          "sources": [
+            {
+              "asset_id": "protein.tsv",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099729/updates/2026-03-23_jfederspiel_ca08c7ac/other/t04_protein_postbridge_ibaq_pd.txt",
+              "sha256": "ca4dc37b764a352d12820e82c4e2e25099feeee3e70d24d12685a34fbe24e8e8",
+              "size": 49345047,
+              "access_terms": "MassIVE dataset CC0-1.0; source numeric table",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Oziolor et al. and Joel D. Federspiel, Pfizer",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=bd0ccc49e0924d14ba14e9ed6ceffe0e",
+                "source_update": "2026-03-23",
+                "terms_verified": "2026-10-12"
+              }
+            },
+            {
+              "asset_id": "search.fasta",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099729/sequence/Human_UP000005640_9606_noisoform.fasta",
+              "sha256": "3793b9bfcc956a278494734bb775a010513f5764d8047fcdb283d2aeaa7fefb8",
+              "size": 13831073,
+              "access_terms": "UniProt Consortium CC-BY-4.0; deposited search FASTA",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "UniProt Consortium",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=bd0ccc49e0924d14ba14e9ed6ceffe0e",
+                "source_update": "deposited original FASTA; UniProt release unspecified",
+                "terms_verified": "2026-10-12"
+              }
+            }
+          ],
+          "citations": [
+            "https://doi.org/10.1038/s41597-026-07512-9",
+            "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=bd0ccc49e0924d14ba14e9ed6ceffe0e",
+            "https://www.uniprot.org/help/license"
+          ],
+          "assay_kinds": [
+            "digest_ms"
+          ],
+          "coverage": {
+            "accession": "MSV000099729",
+            "family": "pfizer-nonclinical-atlas-2026",
+            "measurement_limits": "Intensity quantities; no calibrated copies per cell; no implicit cross-species absolute comparison",
+            "missingness": "NA is missing; zero is measured zero; absent group/sample combinations have no observation",
+            "nc_orf_search": "not established; missing groups do not establish ORF absence",
+            "pooling": "tissue by sex for rodents; tissue for human/dog; individual member IDs unresolved",
+            "reference_limits": "No genomic assembly or UniProt release declared; exact deposited FASTA pinned",
+            "sample_pairing": "RNA and peptide imports pending; no same-material pairing inferred",
+            "search_sequences": 20600,
+            "search_space": "deposited UniProt FASTA without spliced isoforms",
+            "source_counts": {
+              "IBAQ:missing": 9,
+              "IBAQ:positive": 325061,
+              "IBAQ:zero": 632,
+              "absent_matrix_cells": 57322,
+              "assays": 37,
+              "groups": 10352,
+              "rIBAQ:missing": 9,
+              "rIBAQ:positive": 325061,
+              "rIBAQ:zero": 632,
+              "rows": 325702
+            },
+            "source_table": "t04_protein_postbridge_ibaq_pd.txt",
+            "strain_or_breed_reported": null,
+            "target_resolution": "protein_group"
+          },
+          "processing": {
+            "importer": "pfizer-protein-v1",
+            "operations": [
+              "retain native IBAQ and rIBAQ",
+              "preserve NA, zeros and source row/column",
+              "retain transformed Abundance and sumIBAQ as source text",
+              "resolve reported representative in pinned FASTA without assigning group abundance"
+            ],
+            "parameters": {
+              "aggregate_replicates": false,
+              "infer_group_members": false
+            },
+            "software": "orfdata",
+            "source_update": "2026-03-23",
+            "version": "0.6.0"
+          },
+          "schema": "orfdata.measurements.v1"
+        },
+        "distribution": {
+          "access_terms": "Numeric source tables: MassIVE CC0-1.0. UniProt search-record annotations: CC-BY-4.0, attribution to UniProt Consortium. ORFdata transformation code: Apache-2.0.",
+          "redistributable": true,
+          "download_size": 87293488,
+          "download_sha256": "51c48a28f3db7d02154715f07cb8d908cc2898577b526e1275af33f52dda766d",
+          "installed_size": 1464070144,
+          "data_release": "data-pfizer-protein-2026-10-12.1"
+        },
+        "assets": {
+          "dataset.sqlite": {
+            "url": "https://github.com/openvax/orfdata/releases/download/data-pfizer-protein-2026-10-12.1/pfizer-atlas-human-protein-2026-10-12.1.sqlite.gz",
+            "sha256": "e5fc22a9214732a2626c2269ca99c2a576a9ee31d9f94c4b29e430657ddaef04",
+            "size": 1464070144,
+            "decompress": true
+          }
+        }
+      }
+    }
+  },
+  "pfizer-atlas-mouse-protein": {
+    "default_version": "2026-10-12.1",
+    "versions": {
+      "2026-10-12.1": {
+        "manifest": {
+          "dataset_id": "pfizer-atlas-mouse-protein",
+          "version": "2026-10-12.1",
+          "title": "Pfizer/Oziolor mouse native protein-group abundance",
+          "references": [
+            {
+              "taxon_id": 10090,
+              "species": "mouse",
+              "genome_build": null,
+              "annotation_name": "uniprot",
+              "annotation_version": null,
+              "assembly_accession": null,
+              "strain": null,
+              "strain_taxon_id": null,
+              "sequence_sha256": "f6e080958003abfa54718f9465127a8225661fab1ad0738cc9301ad0d0a5c49f",
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": null
+            }
+          ],
+          "sources": [
+            {
+              "asset_id": "protein.tsv",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099754/updates/2026-03-23_jfederspiel_6db4ede2/other/t04_protein_postbridge_ibaq_pd.txt",
+              "sha256": "b627bec35d1f3011e68f3083a9b0fbfac4beec9fd4da975c15bfb590eb9e9659",
+              "size": 94851860,
+              "access_terms": "MassIVE dataset CC0-1.0; source numeric table",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Oziolor et al. and Joel D. Federspiel, Pfizer",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=068ade8643b2433c99b243fd29d5be78",
+                "source_update": "2026-03-23",
+                "terms_verified": "2026-10-12"
+              }
+            },
+            {
+              "asset_id": "search.fasta",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099754/sequence/Mouse_UP000000589_10090_noisoform.fasta",
+              "sha256": "f6e080958003abfa54718f9465127a8225661fab1ad0738cc9301ad0d0a5c49f",
+              "size": 14325720,
+              "access_terms": "UniProt Consortium CC-BY-4.0; deposited search FASTA",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "UniProt Consortium",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=068ade8643b2433c99b243fd29d5be78",
+                "source_update": "deposited original FASTA; UniProt release unspecified",
+                "terms_verified": "2026-10-12"
+              }
+            }
+          ],
+          "citations": [
+            "https://doi.org/10.1038/s41597-026-07512-9",
+            "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=068ade8643b2433c99b243fd29d5be78",
+            "https://www.uniprot.org/help/license"
+          ],
+          "assay_kinds": [
+            "digest_ms"
+          ],
+          "coverage": {
+            "accession": "MSV000099754",
+            "family": "pfizer-nonclinical-atlas-2026",
+            "measurement_limits": "Intensity quantities; no calibrated copies per cell; no implicit cross-species absolute comparison",
+            "missingness": "NA is missing; zero is measured zero; absent group/sample combinations have no observation",
+            "nc_orf_search": "not established; missing groups do not establish ORF absence",
+            "pooling": "tissue by sex for rodents; tissue for human/dog; individual member IDs unresolved",
+            "reference_limits": "No genomic assembly or UniProt release declared; exact deposited FASTA pinned",
+            "sample_pairing": "RNA and peptide imports pending; no same-material pairing inferred",
+            "search_sequences": 21989,
+            "search_space": "deposited UniProt FASTA without spliced isoforms",
+            "source_counts": {
+              "IBAQ:missing": 102,
+              "IBAQ:positive": 615056,
+              "IBAQ:zero": 833,
+              "absent_matrix_cells": 147821,
+              "assays": 63,
+              "groups": 12124,
+              "rIBAQ:missing": 102,
+              "rIBAQ:positive": 615056,
+              "rIBAQ:zero": 833,
+              "rows": 615991
+            },
+            "source_table": "t04_protein_postbridge_ibaq_pd.txt",
+            "strain_or_breed_reported": [
+              "CD1",
+              "C57BL6"
+            ],
+            "target_resolution": "protein_group"
+          },
+          "processing": {
+            "importer": "pfizer-protein-v1",
+            "operations": [
+              "retain native IBAQ and rIBAQ",
+              "preserve NA, zeros and source row/column",
+              "retain transformed Abundance and sumIBAQ as source text",
+              "resolve reported representative in pinned FASTA without assigning group abundance"
+            ],
+            "parameters": {
+              "aggregate_replicates": false,
+              "infer_group_members": false
+            },
+            "software": "orfdata",
+            "source_update": "2026-03-23",
+            "version": "0.6.0"
+          },
+          "schema": "orfdata.measurements.v1"
+        },
+        "distribution": {
+          "access_terms": "Numeric source tables: MassIVE CC0-1.0. UniProt search-record annotations: CC-BY-4.0, attribution to UniProt Consortium. ORFdata transformation code: Apache-2.0.",
+          "redistributable": true,
+          "download_size": 154779449,
+          "download_sha256": "71e0a340b3102a73f2e0e63d0c69258642bcb29386018f4cb8fcc4a9c37be377",
+          "installed_size": 2717151232,
+          "data_release": "data-pfizer-protein-2026-10-12.1"
+        },
+        "assets": {
+          "dataset.sqlite": {
+            "url": "https://github.com/openvax/orfdata/releases/download/data-pfizer-protein-2026-10-12.1/pfizer-atlas-mouse-protein-2026-10-12.1.sqlite.gz",
+            "sha256": "0e1dec8f1ff3bfe1b557816e0360b720cd8106a06cc9573b5a2e9ab1334b1f97",
+            "size": 2717151232,
+            "decompress": true
+          }
+        }
+      }
+    }
+  },
+  "pfizer-atlas-dog-protein": {
+    "default_version": "2026-10-12.1",
+    "versions": {
+      "2026-10-12.1": {
+        "manifest": {
+          "dataset_id": "pfizer-atlas-dog-protein",
+          "version": "2026-10-12.1",
+          "title": "Pfizer/Oziolor dog native protein-group abundance",
+          "references": [
+            {
+              "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": "d8488bf283de653efcff2e5de6d413b116e1ba4a2eb89298bd31205e72fef682",
+              "taxonomy_version": "ncbi-2026-10-12",
+              "source_sha256": null
+            }
+          ],
+          "sources": [
+            {
+              "asset_id": "protein.tsv",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099744/updates/2026-03-23_jfederspiel_6c91304a/other/t04_protein_postbridge_ibaq_pd.txt",
+              "sha256": "ae2953c3fe3c31bc5fa06a9a0b222815376faea25489e6626af3736b7f4cbef2",
+              "size": 48196601,
+              "access_terms": "MassIVE dataset CC0-1.0; source numeric table",
+              "license_url": "https://creativecommons.org/publicdomain/zero/1.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "Oziolor et al. and Joel D. Federspiel, Pfizer",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=062b109e9adf461ba619369dd0d85aa9",
+                "source_update": "2026-03-23",
+                "terms_verified": "2026-10-12"
+              }
+            },
+            {
+              "asset_id": "search.fasta",
+              "url": "https://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?file=f.MSV000099744/sequence/Dog_UP000002254_9615_noisoform.fasta",
+              "sha256": "d8488bf283de653efcff2e5de6d413b116e1ba4a2eb89298bd31205e72fef682",
+              "size": 14659832,
+              "access_terms": "UniProt Consortium CC-BY-4.0; deposited search FASTA",
+              "license_url": "https://creativecommons.org/licenses/by/4.0/",
+              "redistributable": true,
+              "metadata": {
+                "attribution": "UniProt Consortium",
+                "deposit": "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=062b109e9adf461ba619369dd0d85aa9",
+                "source_update": "deposited original FASTA; UniProt release unspecified",
+                "terms_verified": "2026-10-12"
+              }
+            }
+          ],
+          "citations": [
+            "https://doi.org/10.1038/s41597-026-07512-9",
+            "https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=062b109e9adf461ba619369dd0d85aa9",
+            "https://www.uniprot.org/help/license"
+          ],
+          "assay_kinds": [
+            "digest_ms"
+          ],
+          "coverage": {
+            "accession": "MSV000099744",
+            "family": "pfizer-nonclinical-atlas-2026",
+            "measurement_limits": "Intensity quantities; no calibrated copies per cell; no implicit cross-species absolute comparison",
+            "missingness": "NA is missing; zero is measured zero; absent group/sample combinations have no observation",
+            "nc_orf_search": "not established; missing groups do not establish ORF absence",
+            "pooling": "tissue by sex for rodents; tissue for human/dog; individual member IDs unresolved",
+            "reference_limits": "No genomic assembly or UniProt release declared; exact deposited FASTA pinned",
+            "sample_pairing": "RNA and peptide imports pending; no same-material pairing inferred",
+            "search_sequences": 20649,
+            "search_space": "deposited UniProt FASTA without spliced isoforms",
+            "source_counts": {
+              "IBAQ:missing": 8,
+              "IBAQ:positive": 312143,
+              "IBAQ:zero": 1112,
+              "absent_matrix_cells": 64039,
+              "assays": 38,
+              "groups": 9929,
+              "rIBAQ:missing": 8,
+              "rIBAQ:positive": 312143,
+              "rIBAQ:zero": 1112,
+              "rows": 313263
+            },
+            "source_table": "t04_protein_postbridge_ibaq_pd.txt",
+            "strain_or_breed_reported": [
+              "beagle"
+            ],
+            "target_resolution": "protein_group"
+          },
+          "processing": {
+            "importer": "pfizer-protein-v1",
+            "operations": [
+              "retain native IBAQ and rIBAQ",
+              "preserve NA, zeros and source row/column",
+              "retain transformed Abundance and sumIBAQ as source text",
+              "resolve reported representative in pinned FASTA without assigning group abundance"
+            ],
+            "parameters": {
+              "aggregate_replicates": false,
+              "infer_group_members": false
+            },
+            "software": "orfdata",
+            "source_update": "2026-03-23",
+            "version": "0.6.0"
+          },
+          "schema": "orfdata.measurements.v1"
+        },
+        "distribution": {
+          "access_terms": "Numeric source tables: MassIVE CC0-1.0. UniProt search-record annotations: CC-BY-4.0, attribution to UniProt Consortium. ORFdata transformation code: Apache-2.0.",
+          "redistributable": true,
+          "download_size": 84379381,
+          "download_sha256": "5f0c319e8a0584000a68f28099ee685d323bd38ab8ac0c7539907dd82ea44fb4",
+          "installed_size": 1404428288,
+          "data_release": "data-pfizer-protein-2026-10-12.1"
+        },
+        "assets": {
+          "dataset.sqlite": {
+            "url": "https://github.com/openvax/orfdata/releases/download/data-pfizer-protein-2026-10-12.1/pfizer-atlas-dog-protein-2026-10-12.1.sqlite.gz",
+            "sha256": "33d5506874eb32b5426aee7e5d528bb4f754ecf3ac5bc00f5e3fb16fd3ee0694",
+            "size": 1404428288,
+            "decompress": true
+          }
+        }
+      }
+    }
+  }
+}

{orfdata-0.5.0 → orfdata-0.6.0}/orfdata/dataset_cli.py

@@ -18,7 +18,7 @@ def run(argv=None, prog=None):
     listing.add_argument("--species")
     listing.add_argument("--taxon-id", type=int)
     listing.add_argument("--assay")
-    for command in ("info", "download", "inspect", "query", "pairs"):
+    for command in ("info", "download", "build", "inspect", "query", "pairs"):
         subparser = commands.add_parser(command)
         subparser.add_argument("name")
         subparser.add_argument("--version")
@@ -26,7 +26,13 @@ def run(argv=None, prog=None):
             subparser.add_argument("--force", action="store_true")
             subparser.add_argument("--timeout", type=float)
             subparser.add_argument("--quiet", action="store_true")
-            subparser.add_argument("--source-path", help="Use a local dataset.sqlite with the registered hash")
+            subparser.add_argument("--source-path", help="Use a local registered artifact (compressed when declared)")
+        if command == "build":
+            subparser.add_argument("--force", action="store_true")
+            subparser.add_argument("--timeout", type=float)
+            subparser.add_argument("--quiet", action="store_true")
+            subparser.add_argument("--source-path", action="append", default=[], metavar="ASSET=PATH",
+                                   help="Use a local pinned source; repeat for each input asset")
         if command == "query":
             subparser.add_argument("--reference", help="Exact ref:SHA256 context key")
             subparser.add_argument("--sample")
@@ -74,6 +80,20 @@ def run(argv=None, prog=None):
             sources = {"dataset.sqlite": args.source_path} if args.source_path else None
             result = registry.download(args.name, args.version, force=args.force,
                                        source_paths=sources, **options)
+        elif args.command == "build":
+            sources = {}
+            for value in args.source_path:
+                asset, separator, path = value.partition("=")
+                if not separator or not asset or not path or asset in sources:
+                    parser.error("Source overrides require unique ASSET=PATH entries")
+                sources[asset] = path
+            options = dict(show_progress=not args.quiet)
+            if args.timeout is not None:
+                options["timeout"] = args.timeout
+            dataset = registry.build(args.name, args.version, force=args.force,
+                                     source_paths=sources, download_options=options)
+            result = dict(path=str(dataset.path), counts=dataset.counts,
+                          dataset_id=dataset.manifest.dataset_id, version=dataset.manifest.version)
         elif args.command == "pairs":
             dataset = registry.open(args.name, args.version)
             for match in dataset.matched_measurements(

{orfdata-0.5.0 → orfdata-0.6.0}/orfdata/datasets.py

@@ -122,6 +122,16 @@ class DatasetRegistry:
         return self._data_registry().download(name, version, force=force,
                                              source_paths=source_paths, **options)
 
+    def build(self, name, version=None, *, force=False, source_paths=None, download_options=None):
+        """Rebuild a registered release from pinned source files, explicitly."""
+        from .sources import importer
+
+        manifest = self.info(name, version)
+        transform = importer(manifest.processing.get("importer"))
+        return build_dataset(manifest, lambda inputs, output: transform(inputs, output, manifest),
+                             cache_root=self._cache_root, source_paths=source_paths, force=force,
+                             download_options=download_options)
+
     def open(self, name, version=None, *, verify_files=True):
         """Open an installed dataset after integrity and identity checks, offline."""
         version = self._version(name, version)

orfdata-0.6.0/orfdata/sources/__init__.py

@@ -0,0 +1,10 @@
+"""Source-specific importers; source measurements retain their native semantics."""
+
+
+def importer(name):
+    """Resolve a packaged importer, never execute an import path from metadata."""
+    if name == "pfizer-protein-v1":
+        from .pfizer import import_protein
+
+        return import_protein
+    raise ValueError(f"No packaged importer for {name!r}")