Track CGD GPI files as per-species dataset metadata

Replace the six GPI stanzas added to cgd.yaml with one dataset file per
species, following the xenbase_xlae / xenbase_xtro precedent.

- Unwrap Proofpoint URL Defense from all six source URLs. Two of the
  unwrapped URLs (C_albicans_SC5314_with_B_alleles.gpi, C_auris_B8441.gpi)
  404: CGD serves only gzipped GPIs, so all six now point at .gpi.gz.
  This also drops the pasted Outlook HTML attributes that had been
  captured into two of the source values.

- Give each GPI its own "dataset" name. All six previously shared
  "dataset: cgd" with the existing GAF, which collides on the
  <dataset>-src.<type> download path and, in
  download-annotation-sources.py, lets gpi (rank 2) displace the CGD GAF
  (rank 1) outright.

- Drop the "url" fields. They pointed at UniProt-generated GOA mirror
  files under annotations/gpi/ (two of which do not exist) rather than
  at anything CGD produces. Per the xenbase precedent, per-species GPI
  entries carry no url.

- Use go-site 4-character species codes (Calb, Caur, Cdub, Cgla, Cpar,
  Ctro) rather than UniProt mnemonics.

cgd.yaml is returned to its state on master; the combined GAF entry is
untouched.

Refs #2725

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Author: kltm

metadata/datasets/cgd.yaml

@@ -27,94 +27,3 @@ datasets:
     - NCBITaxon:237561
     - NCBITaxon:498019
     - NCBITaxon:294747
- -
-   id: canal.gpi
-   label: "CGD Candida albicans gpi file"
-   description: "gpi file for Candida albicans from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANAL-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_albicans_SC5314_with_B_alleles.gpi__;!!G92We9drHetJ8EofZw!ZdlsxStpibpFJ4VPIMh7Le6dMRxA2ILwhhyiVufoBvaPjzNBpYJXATAL3xa8BOuo2ikNDfOYPblTsFXkY62eQblLp3xe$" id="OWA8a679570-42c1-2fdc-5c3a-dc6c51992fb3
-   entity_type:
-   status: active
-   species_code: CANAL
-   taxa:
-    - NCBITaxon:237561
- -
-   id: canar.gpi
-   label: "CGD Candidozyma auris gpi file"
-   description: "gpi file for Candidozyma auris from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANAR-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_auris_B8441.gpi__;!!G92We9drHetJ8EofZw!ZdlsxStpibpFJ4VPIMh7Le6dMRxA2ILwhhyiVufoBvaPjzNBpYJXATAL3xa8BOuo2ikNDfOYPblTsFXkY62eQVxKRSu5$" id="OWAffa59ccc-558e-f97d-9ce9-759ce796059b" class="x_x_x_x_OWAAutoLink" data-outlook-id="ec6ac22d-13b6-4dc0-bacb-ee5d83d328f4
-   entity_type:
-   status: active
-   species_code: CANAR
-   taxa:
-    - NCBITaxon:498019
- -
-   id: candc.gpi
-   label: "CGD Candida dubliniensis gpi file"
-   description: "gpi file for Candida dubliniensis from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANDC-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_dubliniensis_CD36.gpi.gz__;!!G92We9drHetJ8EofZw!YV1gv8nRePA_R3929JunbAJz1HzKHzy10dZbG4cD0iQOJdPbtD6Q1AFEoG_qRmziRA-kLJH9uaRbYXjdCQT-ZXehv1Rp$
-   entity_type:
-   status: active
-   species_code: CANDC
-   taxa:
-    - NCBITaxon:573826
- -
-   id: canga.gpi
-   label: "CGD Candida glabrata gpi file"
-   description: "gpi file for Candida glabrata from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANGA-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_glabrata_CBS138.gpi.gz__;!!G92We9drHetJ8EofZw!YV1gv8nRePA_R3929JunbAJz1HzKHzy10dZbG4cD0iQOJdPbtD6Q1AFEoG_qRmziRA-kLJH9uaRbYXjdCQT-ZbmCt9oh$
-   entity_type:
-   status: active
-   species_code: CANGA
-   taxa:
-    - NCBITaxon:284593  
- -
-   id: canpc.gpi
-   label: "CGD Candida parapsilosis gpi file"
-   description: "gpi file for Candida parapsilosis from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANPC-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_parapsilosis_CDC317.gpi.gz__;!!G92We9drHetJ8EofZw!YV1gv8nRePA_R3929JunbAJz1HzKHzy10dZbG4cD0iQOJdPbtD6Q1AFEoG_qRmziRA-kLJH9uaRbYXjdCQT-ZWTT4mgC$
-   entity_type:
-   status: active
-   species_code: CANPC
-   taxa:
-    - NCBITaxon:578454
- -
-   id: cantt.gpi
-   label: "CGD Candida tropicalis gpi file"
-   description: "gpi file for Candida tropicalis from CGD"
-   url: http://current.geneontology.org/annotations/gpi/CANTT-mod.gpi.gz
-   type: gpi
-   dataset: cgd
-   submitter: cgd
-   compression: gzip
-   source: https://urldefense.com/v3/__https://www.candidagenome.org/download/go/C_tropicalis.gpi.gz__;!!G92We9drHetJ8EofZw!YV1gv8nRePA_R3929JunbAJz1HzKHzy10dZbG4cD0iQOJdPbtD6Q1AFEoG_qRmziRA-kLJH9uaRbYXjdCQT-ZcqTsSen$
-   entity_type:
-   status: active
-   species_code: CANTT
-   taxa:
-    - NCBITaxon:294747
-    

metadata/datasets/cgd_calb.yaml

@@ -0,0 +1,23 @@
+id: cgd_calb
+label: CGD (albicans)
+description: "GO data for CGD (Candida albicans)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_calb.gpi
+    label: "CGD C. albicans gpi file"
+    description: "gpi file for C. albicans from CGD"
+    type: gpi
+    dataset: cgd_calb
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_albicans_SC5314_with_B_alleles.gpi.gz
+    entity_type:
+    status: active
+    species_code: Calb
+    taxa:
+      - NCBITaxon:237561

metadata/datasets/cgd_caur.yaml

@@ -0,0 +1,23 @@
+id: cgd_caur
+label: CGD (auris)
+description: "GO data for CGD (Candida auris)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_caur.gpi
+    label: "CGD C. auris gpi file"
+    description: "gpi file for C. auris from CGD"
+    type: gpi
+    dataset: cgd_caur
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_auris_B8441.gpi.gz
+    entity_type:
+    status: active
+    species_code: Caur
+    taxa:
+      - NCBITaxon:498019

metadata/datasets/cgd_cdub.yaml

@@ -0,0 +1,23 @@
+id: cgd_cdub
+label: CGD (dubliniensis)
+description: "GO data for CGD (Candida dubliniensis)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_cdub.gpi
+    label: "CGD C. dubliniensis gpi file"
+    description: "gpi file for C. dubliniensis from CGD"
+    type: gpi
+    dataset: cgd_cdub
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_dubliniensis_CD36.gpi.gz
+    entity_type:
+    status: active
+    species_code: Cdub
+    taxa:
+      - NCBITaxon:573826

metadata/datasets/cgd_cgla.yaml

@@ -0,0 +1,23 @@
+id: cgd_cgla
+label: CGD (glabrata)
+description: "GO data for CGD (Candida glabrata)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_cgla.gpi
+    label: "CGD C. glabrata gpi file"
+    description: "gpi file for C. glabrata from CGD"
+    type: gpi
+    dataset: cgd_cgla
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_glabrata_CBS138.gpi.gz
+    entity_type:
+    status: active
+    species_code: Cgla
+    taxa:
+      - NCBITaxon:284593

metadata/datasets/cgd_cpar.yaml

@@ -0,0 +1,23 @@
+id: cgd_cpar
+label: CGD (parapsilosis)
+description: "GO data for CGD (Candida parapsilosis)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_cpar.gpi
+    label: "CGD C. parapsilosis gpi file"
+    description: "gpi file for C. parapsilosis from CGD"
+    type: gpi
+    dataset: cgd_cpar
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_parapsilosis_CDC317.gpi.gz
+    entity_type:
+    status: active
+    species_code: Cpar
+    taxa:
+      - NCBITaxon:578454

metadata/datasets/cgd_ctro.yaml

@@ -0,0 +1,23 @@
+id: cgd_ctro
+label: CGD (tropicalis)
+description: "GO data for CGD (Candida tropicalis)"
+project_name: "Candida Genome Database (CGD)"
+contact_email: "candida-curator@lists.stanford.edu"
+project_url: "http://www.candidagenome.org/"
+funding_source: "NIDCR at US NIH, grant number 1-R01-DE015873-01"
+email_report: "candida-curator@lists.stanford.edu"
+datasets:
+  -
+    id: cgd_ctro.gpi
+    label: "CGD C. tropicalis gpi file"
+    description: "gpi file for C. tropicalis from CGD"
+    type: gpi
+    dataset: cgd_ctro
+    submitter: cgd
+    compression: gzip
+    source: https://www.candidagenome.org/download/go/C_tropicalis.gpi.gz
+    entity_type:
+    status: active
+    species_code: Ctro
+    taxa:
+      - NCBITaxon:294747