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Pattern mismatch warnings during startup #4

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stain opened this issue May 19, 2015 · 0 comments
Open

Pattern mismatch warnings during startup #4

stain opened this issue May 19, 2015 · 0 comments

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@stain
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stain commented May 19, 2015

Investigate if these are anything to worry about:

Registry read in. Now loading DataSources
FullName mismatch for Rf BridgeDb has Rfam while miriam uses RFAM
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000409 was ^RF\d{5}$ but BridgeBD has RF\d+
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000194 was ^[A-Z-0-9]+(?<!CHEBI)(\:)?[A-Za-z0-9+_.%-]+$ but BridgeBD has ^\w+\:[A-Za-z0-9-]+$
FullName mismatch for R BridgeDb has RGD while miriam uses Rat Genome Database
FullName mismatch for X BridgeDb has Affy while miriam uses Affymetrix Probeset
FullName mismatch for S BridgeDb has Uniprot-TrEMBL while miriam uses UniProt Knowledgebase
Alternative mismatch for S BridgeDb has UniProtKB/TrEMBL while miriam uses UniProt Knowledgebase
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000005 was ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ but BridgeBD has ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000003 was ^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ but BridgeBD has ^ENS[A-Z]*[FPTG]\d{11}$
FullName mismatch for drugbankTarget BridgeDb has Drugbank Target while miriam uses DrugBank Target v3
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000044 was ^DIP(\:)?\-\d{1,}[ENXS]$ but BridgeBD has ^DIP[\:\-]\d{3}[EN]$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000042 was ^MINT\-\d{1,7}$ but BridgeBD has ^MINT\-\d{1,5}$
FullName mismatch for Sk BridgeDb has SPIKE while miriam uses SPIKE Map
FullName mismatch for Hac BridgeDb has HGNC Accession number while miriam uses HGNC
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000080 was ^((HGNC|hgnc):)?\d{1,5}$ but BridgeBD has ^(HGNC:)?\d{1,5}$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000161 was ^rs\d+$ but BridgeBD has ^\d+$
FullName mismatch for H BridgeDb has HGNC while miriam uses HGNC Symbol
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000362 was ^[A-Za-z-0-9_]+(\@)?$ but BridgeBD has ^[A-Za-z0-9]+
FullName mismatch for A BridgeDb has TAIR while miriam uses TAIR Locus
FullName mismatch for Bg BridgeDb has BioGrid while miriam uses BioGRID
FullName mismatch for Cs BridgeDb has Chemspider while miriam uses ChemSpider
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000027 was ^(WBGene\d{8}|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ but BridgeBD has ^WBGene\d{8}$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000023 was ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ but BridgeBD has ^S\d+$
FullName mismatch for Pid BridgeDb has NCI Pathway Interaction Database while miriam uses NCI Pathway Interaction Database: Pathway
Alternative mismatch for Pid BridgeDb has NCI Pathway Interaction Database while miriam uses NCI Pathway Interaction Database: Pathway
FullName mismatch for G BridgeDb has GenBank while miriam uses Nucleotide Sequence Database
Alternative mismatch for G BridgeDb has GenBank while miriam uses Nucleotide Sequence Database
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000029 was ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ but BridgeBD has (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5})
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000205 was ^\w+(\.\d+)?(\.\d+)?$ but BridgeBD has ^\w+$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000487 was ^\d+$ but BridgeBD has \d+
FullName mismatch for Cc BridgeDb has CCDS while miriam uses Consensus CDS
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000377 was ^\d+$ but BridgeBD has
FullName mismatch for Em BridgeDb has EMBL while miriam uses ENA
Alternative mismatch for Em BridgeDb has European Nucleotide Archive while miriam uses ENA
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000437 was ^\d+$ but BridgeBD has
FullName mismatch for L BridgeDb has Entrez Gene while miriam uses NCBI Gene
Alternative mismatch for L BridgeDb has Entrez Gene while miriam uses NCBI Gene
FullName mismatch for T BridgeDb has GeneOntology while miriam uses Gene Ontology
FullName mismatch for Pd BridgeDb has PDB while miriam uses Protein Data Bank
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000344 was ^(\w+\d+(\.\d+)?)|(NP_\d+)$ but BridgeBD has ^\w+\d+(\.\d+)?$
FullName mismatch for unigene BridgeDb has UniGene number while miriam uses UniGene
FullName mismatch for M BridgeDb has MGI while miriam uses Mouse Genome Database
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000039 was ^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$ but BridgeBD has ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$
FullName mismatch for Tb BridgeDb has TubercuList while miriam uses MycoBrowser tuberculosis
Alternative mismatch for Tb BridgeDb has TubercuList while miriam uses MycoBrowser tuberculosis
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000216 was ^Rv\d{4}(A|B|c)?$ but BridgeBD has Rv\d{4}(A|B|c|\.\d)?
FullName mismatch for Gg BridgeDb has Gramene Genes DB while miriam uses Gramene genes
Alternative mismatch for Gg BridgeDb has Gramene Genes while miriam uses Gramene genes
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000182 was ^GR\:\d+$ but BridgeBD has GR:\d+
FullName mismatch for drugbankv4.target BridgeDb has Drugbank Target v4 while miriam uses DrugBank Target v4
FullName mismatch for Wi BridgeDb has Wikipedia while miriam uses Wikipedia (En)
Alternative mismatch for Wi BridgeDb has Wikipedia while miriam uses Wikipedia (En)
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000384 was ^[A-Za-z-0-9_]+$ but BridgeBD has
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000076 was WP\d{1,5}(\_r\d+)?$ but BridgeBD has WP\d{1,5}(_r\d+)?
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000027 was ^(WBGene\d{8}|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ but BridgeBD has ^WBGene\d{8}$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000023 was ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ but BridgeBD has ^S\d+$
FullName mismatch for Pid BridgeDb has NCI Pathway Interaction Database while miriam uses NCI Pathway Interaction Database: Pathway
Alternative mismatch for Pid BridgeDb has NCI Pathway Interaction Database while miriam uses NCI Pathway Interaction Database: Pathway
FullName mismatch for G BridgeDb has GenBank while miriam uses Nucleotide Sequence Database
Alternative mismatch for G BridgeDb has GenBank while miriam uses Nucleotide Sequence Database
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000029 was ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ but BridgeBD has (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5})
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000205 was ^\w+(\.\d+)?(\.\d+)?$ but BridgeBD has ^\w+$
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000487 was ^\d+$ but BridgeBD has \d+
FullName mismatch for Cc BridgeDb has CCDS while miriam uses Consensus CDS
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000377 was ^\d+$ but BridgeBD has
FullName mismatch for Em BridgeDb has EMBL while miriam uses ENA
Alternative mismatch for Em BridgeDb has European Nucleotide Archive while miriam uses ENA
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000437 was ^\d+$ but BridgeBD has
FullName mismatch for L BridgeDb has Entrez Gene while miriam uses NCBI Gene
Alternative mismatch for L BridgeDb has Entrez Gene while miriam uses NCBI Gene
FullName mismatch for T BridgeDb has GeneOntology while miriam uses Gene Ontology
FullName mismatch for Pd BridgeDb has PDB while miriam uses Protein Data Bank
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000344 was ^(\w+\d+(\.\d+)?)|(NP_\d+)$ but BridgeBD has ^\w+\d+(\.\d+)?$
FullName mismatch for unigene BridgeDb has UniGene number while miriam uses UniGene
FullName mismatch for M BridgeDb has MGI while miriam uses Mouse Genome Database
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000039 was ^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$ but BridgeBD has ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$
FullName mismatch for Tb BridgeDb has TubercuList while miriam uses MycoBrowser tuberculosis
Alternative mismatch for Tb BridgeDb has TubercuList while miriam uses MycoBrowser tuberculosis
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000216 was ^Rv\d{4}(A|B|c)?$ but BridgeBD has Rv\d{4}(A|B|c|\.\d)?
FullName mismatch for Gg BridgeDb has Gramene Genes DB while miriam uses Gramene genes
Alternative mismatch for Gg BridgeDb has Gramene Genes while miriam uses Gramene genes
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000182 was ^GR\:\d+$ but BridgeBD has GR:\d+
FullName mismatch for drugbankv4.target BridgeDb has Drugbank Target v4 while miriam uses DrugBank Target v4
FullName mismatch for Wi BridgeDb has Wikipedia while miriam uses Wikipedia (En)
Alternative mismatch for Wi BridgeDb has Wikipedia while miriam uses Wikipedia (En)
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000384 was ^[A-Za-z-0-9_]+$ but BridgeBD has
Regex patterns do not match for http://www.ebi.ac.uk/miriam/main/collections/MIR:00000076 was WP\d{1,5}(\_r\d+)?$ but BridgeBD has WP\d{1,5}(_r\d+)?
FullName mismatch for Z BridgeDb has ZFIN while miriam uses ZFIN Gene
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