forked from OBOFoundry/purl.obolibrary.org
-
Notifications
You must be signed in to change notification settings - Fork 0
/
obo.yml
170 lines (137 loc) · 5.87 KB
/
obo.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
# PURL configuration for http://purl.obolibrary.org/obo/
idspace: OBO
base_url: /obo
term_browser: custom
### Global Tests
tests:
# Test case insensitivity
- from: /chebi/about/CHEBI_15377
to: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_15377
- from: /CHEBI/about/CHEBI_15377
to: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_15377
### Entries
entries:
### Term Overrides
- exact: /BFO_0000050
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000050
- exact: /BFO_0000051
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000051
- exact: /BFO_0000054
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000054
- exact: /BFO_0000055
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000055
- exact: /BFO_0000062
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000062
- exact: /BFO_0000063
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000063
- exact: /BFO_0000066
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000066
- exact: /BFO_0000067
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/BFO_0000067
### Custom (non-Ontobee) term_browser redirects
# Term redirects for DUO
- regex: ^/obo/DUO_(\d+)$
replacement: https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http://purl.obolibrary.org/obo/DUO_$1
status: see other
tests:
- from: /DUO_0000005
to: https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http://purl.obolibrary.org/obo/DUO_0000005
# Term redirects for MONDO
- regex: ^/obo/MONDO_(\d+)$
replacement: https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/MONDO_$1
status: see other
tests:
- from: /MONDO_0003847
to: https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/MONDO_0003847
# Term redirects for CHEBI
- regex: ^/obo/CHEBI_(\d+)$
replacement: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
status: see other
tests:
- from: /CHEBI_15377
to: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377
# Term redirects for GO
- regex: ^/obo/GO_(\d+)$
replacement: http://amigo.geneontology.org/amigo/term/GO:$1
status: see other
tests:
- from: /GO_0032571
to: http://amigo.geneontology.org/amigo/term/GO:0032571
# Term redirects for HP
- regex: ^/obo/HP_(\d+)$
replacement: https://hpo.jax.org/app/browse/term/HP:$1
status: see other
tests:
- from: /HP_0002088
to: https://hpo.jax.org/app/browse/term/HP:0002088
# Term redirects for FLOPO
- regex: ^/obo/FLOPO_(\d+)$
replacement: http://aber-owl.net/ontology/FLOPO#!http://purl.obolibrary.org/obo/FLOPO_$1
status: see other
tests:
- from: /FLOPO_0000000
to: http://aber-owl.net/ontology/FLOPO#!http://purl.obolibrary.org/obo/FLOPO_0000000
# Term redirects for HAO
- regex: ^/obo/HAO_(\d+)$
replacement: http://api.hymao.org/api/ontology/ontology_class/HAO_$1
status: see other
tests:
- from: /HAO_0000000
to: http://api.hymao.org/api/ontology/ontology_class/HAO_0000000
# Term redirects for PR
# Match digits or UniProt ID, see http://www.uniprot.org/help/accession_numbers
- regex: ^/obo/PR_(\d+|[OPQ][0-9][A-Z0-9]{3}[0-9](-\d+)?|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}(-\d+)?)$
replacement: https://proconsortium.org/cgi-bin/entry_pro?id=PR_$1
status: see other
tests:
- from: /PR_000000001
to: https://proconsortium.org/cgi-bin/entry_pro?id=PR_000000001
- from: /PR_Q9BWV1
to: https://proconsortium.org/cgi-bin/entry_pro?id=PR_Q9BWV1
- from: /PR_P20263-1
to: https://proconsortium.org/cgi-bin/entry_pro?id=PR_P20263-1
- from: /PR_A0A0E0NEP8
to: https://proconsortium.org/cgi-bin/entry_pro?id=PR_A0A0E0NEP8
- from: /PR_A0A0E0NEP8-37
to: https://proconsortium.org/cgi-bin/entry_pro?id=PR_A0A0E0NEP8-37
# Term redirects for RO
# Some RO terms have a local ID starting with an alphanumeric character, e.g RO_HOMnnnnn
- regex: ^/obo/RO_([A-Z]*\d+)$
replacement: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_$1
status: see other
tests:
- from: /RO_0002202
to: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_0002202
- from: /RO_HOM0000001
to: https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_HOM0000001
# Term redirects for GNO
# Match digits or GlyTouCan ID
- regex: ^/obo/GNO_(\d+|G[0-9]{5}[A-Z]{2})$
replacement: http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_$1
status: see other
tests:
- from: /GNO_00000001
to: http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001
- from: /GNO_G00982CE
to: http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_G00982CE
# Term redirects for NCIT (not restricted to digits)
- regex: ^/obo/NCIT_([a-zA-Z0-9]+)$
replacement: http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_$1
status: see other
tests:
- from: /NCIT_C2916
to: http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C2916
# Term redirects for DOID
- regex: ^/obo/DOID_(\d+)$
replacement: https://disease-ontology.org/?id=DOID:$1
status: see other
tests:
- from: /DOID_4
to: https://disease-ontology.org/?id=DOID:4
- from: /DOID_0014667
to: https://disease-ontology.org/?id=DOID:0014667
### OBO Format Specification
- exact: /oboformat/
replacement: http://owlcollab.github.io/oboformat/doc/obo-syntax.html
- exact: /oboformat/spec.html
replacement: http://owlcollab.github.io/oboformat/doc/obo-syntax.html