-
Notifications
You must be signed in to change notification settings - Fork 18
/
clashes.txt
213 lines (213 loc) · 28.7 KB
/
clashes.txt
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
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
INFO:root:Files: ('registry/go_context.jsonld', 'registry/idot_context.jsonld', 'registry/semweb_context.jsonld', 'registry/monarch_context.jsonld', 'registry/semweb_vocab_context.jsonld', 'registry/ro_vocab_context.jsonld', 'registry/obo_context.jsonld')
INFO:root:CANONICAL FILE: registry/go_context.jsonld
WARNING:root:URI clash: http://purl.obolibrary.org/obo/BTO_ is expansion for BTO and BTO
WARNING:root:Prefix clash: BTO Was=http://purl.obolibrary.org/obo/BTO_ [registry/go_context.jsonld], Now=http://identifiers.org/bto/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/CL_ is expansion for CL and CL
WARNING:root:Prefix clash: CL Was=http://purl.obolibrary.org/obo/CL_ [registry/go_context.jsonld], Now=http://identifiers.org/cl/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/PATO_ is expansion for PATO and PATO
WARNING:root:Prefix clash: PATO Was=http://purl.obolibrary.org/obo/PATO_ [registry/go_context.jsonld], Now=http://identifiers.org/pato/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/rgd/ is expansion for RGD and RGD
WARNING:root:URI clash: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN= is expansion for SMART and SMART
WARNING:root:Prefix clash: SMART Was=http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN= [registry/go_context.jsonld], Now=http://identifiers.org/smart/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid= is expansion for CDD and CDD
WARNING:root:Prefix clash: CDD Was=http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid= [registry/go_context.jsonld], Now=http://identifiers.org/cdd/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/ensembl/ is expansion for ENSEMBL and ENSEMBL
WARNING:root:URI clash: http://purl.obolibrary.org/obo/SO_ is expansion for SO and SO
WARNING:root:Prefix clash: SO Was=http://purl.obolibrary.org/obo/SO_ [registry/go_context.jsonld], Now=http://identifiers.org/so/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.rhea-db.org/reaction.xhtml?id= is expansion for RHEA and RHEA
WARNING:root:Prefix clash: RHEA Was=http://www.rhea-db.org/reaction.xhtml?id= [registry/go_context.jsonld], Now=http://identifiers.org/rhea/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/CHEBI_ is expansion for CHEBI and CHEBI
WARNING:root:Prefix clash: CHEBI Was=http://purl.obolibrary.org/obo/CHEBI_ [registry/go_context.jsonld], Now=http://identifiers.org/chebi/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/hgnc/ is expansion for HGNC and HGNC
WARNING:root:URI clash: http://identifiers.org/cas/ is expansion for CAS and CAS
WARNING:root:URI clash: http://www.ecogene.org/geneInfo.php?eg_id= is expansion for ECOGENE and ECOGENE
WARNING:root:Prefix clash: ECOGENE Was=http://www.ecogene.org/geneInfo.php?eg_id= [registry/go_context.jsonld], Now=http://identifiers.org/ecogene/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/RO_ is expansion for RO and RO
WARNING:root:Prefix clash: RO Was=http://purl.obolibrary.org/obo/RO_ [registry/go_context.jsonld], Now=http://identifiers.org/ro/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid= is expansion for MEROPS and MEROPS
WARNING:root:Prefix clash: MEROPS Was=http://merops.sanger.ac.uk/cgi-bin/pepsum?mid= [registry/go_context.jsonld], Now=http://identifiers.org/merops/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/PO_ is expansion for PO and PO
WARNING:root:Prefix clash: PO Was=http://purl.obolibrary.org/obo/PO_ [registry/go_context.jsonld], Now=http://identifiers.org/po/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/tgd/ is expansion for TGD and TGD
WARNING:root:URI clash: http://vbrc.org/query.asp?web_id=VBRC: is expansion for VBRC and VBRC
WARNING:root:Prefix clash: VBRC Was=http://vbrc.org/query.asp?web_id=VBRC: [registry/go_context.jsonld], Now=http://identifiers.org/vbrc/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/UBERON_ is expansion for UBERON and UBERON
WARNING:root:Prefix clash: UBERON Was=http://purl.obolibrary.org/obo/UBERON_ [registry/go_context.jsonld], Now=http://identifiers.org/uberon/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/MA_ is expansion for MA and MA
WARNING:root:Prefix clash: MA Was=http://purl.obolibrary.org/obo/MA_ [registry/go_context.jsonld], Now=http://identifiers.org/ma/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.jstor.org/stable/ is expansion for JSTOR and JSTOR
WARNING:root:Prefix clash: JSTOR Was=http://www.jstor.org/stable/ [registry/go_context.jsonld], Now=http://identifiers.org/jstor/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://dx.doi.org/ is expansion for DOI and DOI
WARNING:root:Prefix clash: DOI Was=http://dx.doi.org/ [registry/go_context.jsonld], Now=http://identifiers.org/doi/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/ECO_ is expansion for ECO and ECO
WARNING:root:Prefix clash: ECO Was=http://purl.obolibrary.org/obo/ECO_ [registry/go_context.jsonld], Now=http://identifiers.org/eco/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id= is expansion for CORUM and CORUM
WARNING:root:Prefix clash: CORUM Was=http://mips.gsf.de/genre/proj/corum/complexdetails.html?id= [registry/go_context.jsonld], Now=http://identifiers.org/corum/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://pir.georgetown.edu/cgi-bin/ipcSF?id= is expansion for PIRSF and PIRSF
WARNING:root:Prefix clash: PIRSF Was=http://pir.georgetown.edu/cgi-bin/ipcSF?id= [registry/go_context.jsonld], Now=http://identifiers.org/pirsf/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.theseed.org/linkin.cgi?id= is expansion for SEED and SEED
WARNING:root:Prefix clash: SEED Was=http://www.theseed.org/linkin.cgi?id= [registry/go_context.jsonld], Now=http://identifiers.org/seed/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc= is expansion for GEO and GEO
WARNING:root:Prefix clash: GEO Was=http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc= [registry/go_context.jsonld], Now=http://identifiers.org/geo/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/wormbase/ is expansion for WB and WB
WARNING:root:Prefix clash: WB Was=http://identifiers.org/wormbase/ [registry/go_context.jsonld], Now=http://identifiers.org/wb/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/sgd/ is expansion for SGD and SGD
WARNING:root:URI clash: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID= is expansion for ASAP and ASAP
WARNING:root:Prefix clash: ASAP Was=https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID= [registry/go_context.jsonld], Now=http://identifiers.org/asap/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.proteinatlas.org/tissue_profile.php?antibody_id= is expansion for HPA and HPA
WARNING:root:Prefix clash: HPA Was=http://www.proteinatlas.org/tissue_profile.php?antibody_id= [registry/go_context.jsonld], Now=http://identifiers.org/hpa/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://mged.sourceforge.net/ontologies/MGEDontology.php# is expansion for MO and MO
WARNING:root:Prefix clash: MO Was=http://mged.sourceforge.net/ontologies/MGEDontology.php# [registry/go_context.jsonld], Now=http://identifiers.org/mo/ [registry/idot_context.jsonld]
WARNING:root:URI clash: https://www.worldcat.org/search?q=bn%3A is expansion for ISBN and ISBN
WARNING:root:Prefix clash: ISBN Was=https://www.worldcat.org/search?q=bn%3A [registry/go_context.jsonld], Now=http://identifiers.org/isbn/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref= is expansion for CORIELL and CORIELL
WARNING:root:Prefix clash: CORIELL Was=http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref= [registry/go_context.jsonld], Now=http://identifiers.org/coriell/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/FMA_ is expansion for FMA and FMA
WARNING:root:Prefix clash: FMA Was=http://purl.obolibrary.org/obo/FMA_ [registry/go_context.jsonld], Now=http://identifiers.org/fma/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn= is expansion for PRINTS and PRINTS
WARNING:root:Prefix clash: PRINTS Was=http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn= [registry/go_context.jsonld], Now=http://identifiers.org/prints/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/GO_ is expansion for GO and GO
WARNING:root:Prefix clash: GO Was=http://purl.obolibrary.org/obo/GO_ [registry/go_context.jsonld], Now=http://identifiers.org/go/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId= is expansion for PDB and PDB
WARNING:root:Prefix clash: PDB Was=http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId= [registry/go_context.jsonld], Now=http://identifiers.org/pdb/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/mgi/MGI: is expansion for MGI and MGI
WARNING:root:Prefix clash: MGI Was=http://identifiers.org/mgi/MGI: [registry/go_context.jsonld], Now=http://identifiers.org/mgi/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/sgn/ is expansion for SGN and SGN
WARNING:root:URI clash: http://identifiers.org/cgd/ is expansion for CGD and CGD
WARNING:root:URI clash: http://hamap.expasy.org/unirule/ is expansion for HAMAP and HAMAP
WARNING:root:Prefix clash: HAMAP Was=http://hamap.expasy.org/unirule/ [registry/go_context.jsonld], Now=http://identifiers.org/hamap/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/zfin/ is expansion for ZFIN and ZFIN
WARNING:root:URI clash: http://identifiers.org/flybase/ is expansion for FB and FB
WARNING:root:Prefix clash: FB Was=http://identifiers.org/flybase/ [registry/go_context.jsonld], Now=http://identifiers.org/fb/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/PR_ is expansion for PR and PR
WARNING:root:Prefix clash: PR Was=http://purl.obolibrary.org/obo/PR_ [registry/go_context.jsonld], Now=http://identifiers.org/pr/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://www.brenda-enzymes.info/php/result_flat.php4?ecno= is expansion for BRENDA and BRENDA
WARNING:root:Prefix clash: BRENDA Was=http://www.brenda-enzymes.info/php/result_flat.php4?ecno= [registry/go_context.jsonld], Now=http://identifiers.org/brenda/ [registry/idot_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/BFO_ is expansion for BFO and BFO
WARNING:root:Prefix clash: BIOGRID Was=http://identifiers.org/biogrid/ [registry/idot_context.jsonld], Now=http://thebiogrid.org/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: CCDS Was=http://identifiers.org/ccds/ [registry/idot_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: CHEBI Was=http://identifiers.org/chebi/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/CHEBI_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: CL Was=http://identifiers.org/cl/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/CL_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: COSMIC Was=http://identifiers.org/cosmic/ [registry/idot_context.jsonld], Now=http://cancer.sanger.ac.uk/cosmic/mutation/overview?id= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: DOI Was=http://identifiers.org/doi/ [registry/idot_context.jsonld], Now=http://dx.doi.org/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: DOID Was=http://identifiers.org/doid/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/DOID_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.expasy.org/enzyme/ is expansion for EC and EC
WARNING:root:Prefix clash: EC Was=http://www.expasy.org/enzyme/ [registry/go_context.jsonld], Now=http://www.enzyme-database.org/query.php?ec= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: ECO Was=http://identifiers.org/eco/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/ECO_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: EFO Was=http://identifiers.org/efo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/EFO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/EMAPA_ is expansion for EMAPA and EMAPA
WARNING:root:URI clash: http://identifiers.org/ensembl/ is expansion for ENSEMBL and ENSEMBL
WARNING:root:Prefix clash: ENSEMBL Was=http://identifiers.org/ensembl/ [registry/idot_context.jsonld], Now=http://ensembl.org/id/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: ENVO Was=http://identifiers.org/envo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/ENVO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/FBbt_ is expansion for FBbt and FBbt
WARNING:root:Prefix clash: GO Was=http://identifiers.org/go/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/GO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/go/references/ is expansion for GO_REF and GO_REF
WARNING:root:Prefix clash: GO_REF Was=http://purl.obolibrary.org/obo/go/references/ [registry/go_context.jsonld], Now=http://www.geneontology.org/cgi-bin/references.cgi#GO_REF: [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val= is expansion for GenBank and GenBank
WARNING:root:Prefix clash: GenBank Was=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val= [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/nuccore/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: HGMD Was=http://identifiers.org/hgmd/ [registry/idot_context.jsonld], Now=http://www.hgmd.cf.ac.uk/ac/gene.php?gene= [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/hgnc/ is expansion for HGNC and HGNC
WARNING:root:Prefix clash: HGNC Was=http://identifiers.org/hgnc/ [registry/idot_context.jsonld], Now=http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: HMDB Was=http://identifiers.org/hmdb/ [registry/idot_context.jsonld], Now=http://www.hmdb.ca/metabolites/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: HOMOLOGENE Was=http://identifiers.org/homologene/ [registry/idot_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/homologene/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: HP Was=http://identifiers.org/hp/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/HP_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: HPRD Was=http://identifiers.org/hprd/ [registry/idot_context.jsonld], Now=http://www.hprd.org/protein/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: IAO Was=http://identifiers.org/iao/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/IAO_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: ISBN Was=http://identifiers.org/isbn/ [registry/idot_context.jsonld], Now=https://monarchinitiative.org/ISBN_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MA Was=http://identifiers.org/ma/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MA_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MEDDRA Was=http://identifiers.org/meddra/ [registry/idot_context.jsonld], Now=http://purl.bioontology.org/ontology/MEDDRA/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MESH Was=http://identifiers.org/mesh/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MESH_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MGI Was=http://identifiers.org/mgi/ [registry/idot_context.jsonld], Now=http://www.informatics.jax.org/accession/MGI: [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MMRRC Was=http://identifiers.org/mmrrc/ [registry/idot_context.jsonld], Now=https://www.mmrrc.org/catalog/sds.php?mmrrc_id= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: MP Was=http://identifiers.org/mp/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MP_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/ncbigene/ is expansion for NCBIGene and NCBIGene
WARNING:root:Prefix clash: NCBIGene Was=http://identifiers.org/ncbigene/ [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/gene/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/NCBITaxon_ is expansion for NCBITaxon and NCBITaxon
WARNING:root:Prefix clash: NCIT Was=http://identifiers.org/ncit/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/NCIT_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: OBI Was=http://identifiers.org/obi/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/OBI_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: OMIA Was=http://identifiers.org/omia/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/OMIA_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://omim.org/entry/ is expansion for OMIM and OMIM
WARNING:root:Prefix clash: OMIM Was=http://omim.org/entry/ [registry/go_context.jsonld], Now=http://purl.obolibrary.org/obo/OMIM_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR is expansion for PAINT_REF and PAINT_REF
WARNING:root:Prefix clash: PAINT_REF Was=http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR [registry/go_context.jsonld], Now=http://www.geneontology.org/gene-associations/submission/paint/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/panther.family/ is expansion for PANTHER and PANTHER
WARNING:root:Prefix clash: PANTHER Was=http://identifiers.org/panther.family/ [registry/go_context.jsonld], Now=http://www.pantherdb.org/panther/family.do?clsAccession= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: PATO Was=http://identifiers.org/pato/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/PATO_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: PDB Was=http://identifiers.org/pdb/ [registry/idot_context.jsonld], Now=http://www.ebi.ac.uk/pdbsum/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term= is expansion for PMCID and PMCID
WARNING:root:Prefix clash: PMCID Was=http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term= [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/pmc/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/pubmed/ is expansion for PMID and PMID
WARNING:root:Prefix clash: PR Was=http://identifiers.org/pr/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/PR_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: PW Was=http://identifiers.org/pw/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/PW_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/pombase/ is expansion for PomBase and PomBase
WARNING:root:Prefix clash: PomBase Was=http://identifiers.org/pombase/ [registry/go_context.jsonld], Now=https://www.pombase.org/spombe/result/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/rgd/ is expansion for RGD and RGD
WARNING:root:Prefix clash: RGD Was=http://identifiers.org/rgd/ [registry/idot_context.jsonld], Now=http://rgd.mcw.edu/rgdweb/report/gene/main.html?id= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: RO Was=http://identifiers.org/ro/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/RO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val= is expansion for RefSeq and RefSeq
WARNING:root:Prefix clash: RefSeq Was=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val= [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/refseq/?term= [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/sgd/ is expansion for SGD and SGD
WARNING:root:Prefix clash: SGD Was=http://identifiers.org/sgd/ [registry/idot_context.jsonld], Now=https://www.yeastgenome.org/locus/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: SMPDB Was=http://identifiers.org/smpdb/ [registry/idot_context.jsonld], Now=http://smpdb.ca/view/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: SO Was=http://identifiers.org/so/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/SO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/tair.locus/ is expansion for TAIR and TAIR
WARNING:root:Prefix clash: TAIR Was=http://identifiers.org/tair.locus/ [registry/go_context.jsonld], Now=https://www.arabidopsis.org/servlets/TairObject?type=locus&id= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: UBERON Was=http://identifiers.org/uberon/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/UBERON_ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: UMLS Was=http://identifiers.org/umls/ [registry/idot_context.jsonld], Now=http://linkedlifedata.com/resource/umls/id/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: UNII Was=http://identifiers.org/unii/ [registry/idot_context.jsonld], Now=http://fdasis.nlm.nih.gov/srs/unii/ [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: UO Was=http://identifiers.org/uo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/UO_ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/uniprot/ is expansion for UniProtKB and UniProtKB
WARNING:root:URI clash: http://purl.obolibrary.org/obo/WBPhenotype_ is expansion for WBPhenotype and WBPhenotype
WARNING:root:URI clash: http://identifiers.org/xenbase/ is expansion for Xenbase and Xenbase
WARNING:root:Prefix clash: Xenbase Was=http://identifiers.org/xenbase/ [registry/go_context.jsonld], Now=http://www.xenbase.org/gene/showgene.do?method=display&geneId= [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/zfin/ is expansion for ZFIN and ZFIN
WARNING:root:Prefix clash: ZFIN Was=http://identifiers.org/zfin/ [registry/idot_context.jsonld], Now=http://zfin.org/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://identifiers.org/dbsnp/ is expansion for dbSNP and dbSNP
WARNING:root:Prefix clash: dbSNP Was=http://identifiers.org/dbsnp/ [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs= [registry/monarch_context.jsonld]
WARNING:root:Prefix clash: dc Was=http://purl.org/dc/terms/ [registry/semweb_context.jsonld], Now=http://purl.org/dc/elements/1.1/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://purl.org/dc/terms/ is expansion for dcterms and dc
WARNING:root:URI clash: http://identifiers.org/dictybase.gene/ is expansion for dictyBase and dictyBase
WARNING:root:Prefix clash: dictyBase Was=http://identifiers.org/dictybase.gene/ [registry/go_context.jsonld], Now=http://dictybase.org/gene/ [registry/monarch_context.jsonld]
WARNING:root:URI clash: http://www.w3.org/2001/XMLSchema# is expansion for xsd and xsd
WARNING:root:Prefix clash: dc Was=http://purl.org/dc/elements/1.1/ [registry/monarch_context.jsonld], Now=http://purl.org/dc/terms/ [registry/semweb_vocab_context.jsonld]
WARNING:root:URI clash: http://www.w3.org/ns/dcat# is expansion for dcat and dcat
WARNING:root:URI clash: http://www.w3.org/2002/07/owl# is expansion for owl and owl
WARNING:root:URI clash: http://xmlns.com/foaf/0.1/ is expansion for foaf and foaf
WARNING:root:URI clash: http://www.w3.org/2000/01/rdf-schema# is expansion for rdfs and rdfs
WARNING:root:URI clash: http://www.w3.org/1999/02/22-rdf-syntax-ns# is expansion for rdf and rdf
WARNING:root:URI clash: http://purl.obolibrary.org/obo/BFO_ is expansion for BFO and BFO
WARNING:root:URI clash: http://purl.obolibrary.org/obo/RO_ is expansion for RO and RO
WARNING:root:Prefix clash: ADW Was=http://identifiers.org/adw/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/ADW_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/BFO_ is expansion for BFO and BFO
WARNING:root:Prefix clash: BTO Was=http://identifiers.org/bto/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/BTO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/CHEBI_ is expansion for CHEBI and CHEBI
WARNING:root:URI clash: http://purl.obolibrary.org/obo/CL_ is expansion for CL and CL
WARNING:root:Prefix clash: DC_CL Was=http://purl.obolibrary.org/obo/DC_CL [registry/monarch_context.jsonld], Now=http://purl.obolibrary.org/obo/DC_CL_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/DDANAT_ is expansion for DDANAT and DDANAT
WARNING:root:URI clash: http://purl.obolibrary.org/obo/ECO_ is expansion for ECO and ECO
WARNING:root:URI clash: http://purl.obolibrary.org/obo/EMAPA_ is expansion for EMAPA and EMAPA
WARNING:root:Prefix clash: EO Was=http://identifiers.org/eo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/EO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/FBbt_ is expansion for FBbt and FBbt
WARNING:root:Prefix clash: FMA Was=http://identifiers.org/fma/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/FMA_ [registry/obo_context.jsonld]
WARNING:root:Prefix clash: FOODON Was=http://identifiers.org/foodon/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/FOODON_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/FYPO_ is expansion for FYPO and FYPO
WARNING:root:Prefix clash: GEO Was=http://identifiers.org/geo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/GEO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/GO_ is expansion for GO and GO
WARNING:root:URI clash: http://purl.obolibrary.org/obo/MA_ is expansion for MA and MA
WARNING:root:Prefix clash: MAMO Was=http://identifiers.org/mamo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MAMO_ [registry/obo_context.jsonld]
WARNING:root:Prefix clash: MO Was=http://identifiers.org/mo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MO_ [registry/obo_context.jsonld]
WARNING:root:Prefix clash: MOD Was=http://identifiers.org/mod/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MOD_ [registry/obo_context.jsonld]
WARNING:root:Prefix clash: MS Was=http://identifiers.org/ms/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MS_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/NCBITaxon_ is expansion for NCBITaxon and NCBITaxon
WARNING:root:Prefix clash: NMR Was=http://identifiers.org/nmr/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/NMR_ [registry/obo_context.jsonld]
WARNING:root:Prefix clash: OMIT Was=http://identifiers.org/omit/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/OMIT_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/PATO_ is expansion for PATO and PATO
WARNING:root:Prefix clash: PO Was=http://identifiers.org/po/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/PO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/PR_ is expansion for PR and PR
WARNING:root:Prefix clash: RESID Was=http://identifiers.org/resid/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/RESID_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/RO_ is expansion for RO and RO
WARNING:root:Prefix clash: SBO Was=http://identifiers.org/sbo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/SBO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/SO_ is expansion for SO and SO
WARNING:root:URI clash: http://purl.obolibrary.org/obo/UBERON_ is expansion for UBERON and UBERON
WARNING:root:Prefix clash: VARIO Was=http://identifiers.org/vario/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/VARIO_ [registry/obo_context.jsonld]
WARNING:root:URI clash: http://purl.obolibrary.org/obo/WBPhenotype_ is expansion for WBPhenotype and WBPhenotype