Inconsistent patterns in several entries

[cthoyt]

This PR points out several entries in identifiers.org with malformed patterns based on the lack of a ^ in the beginning of the pattern or a lacking $ in the end of the pattern. There are a few examples where this actually makes sense, but they are pretty uncommon so it makes it difficult to rely on a given regular expression pattern, which is in some ways necessary to deal with embedded LUIs.

prefix	pattern	^	$
reactome	(^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$)	x	x
signaling-gateway	A\d{6}$	x
eco	ECO:\d{7}$	x
mod	^MOD:\d{5}		x
wikipathways	WP\d{1,5}(\_r\d+)?$	x
mirbase	MI\d{7}	x	x
obi	(^OBI:\d{7}$)|(^OBI_\d{7}$)	x	x
uo	^UO:\d{7}?		x
pmc	PMC\d+	x	x
cryptodb	^\w+		x
tritrypdb	^\w+(\.)?\w+(\.)?\w+		x
pmdb	^PM\d{7}		x
mirbase.mature	MIMAT\d{7}	x	x
nextprot	^NX_\w+		x
worfdb	^\w+(\.\d+)?		x
sdbs	\d+$	x
tarbase	^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?		x
inchikey	^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?		x
affy.probeset	\d{4,}((_[asx])?_at)?	x	x
pocketome	^[A-Za-z_0-9]+		x
ndc	^\d+\-\d+\-\d+		x
dailymed	^[A-Za-z0-9-]+		x
lincs.cell	(^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$)	x	x
d1id	\S+	x	x
vmhmetabolite	[a-zA-Z0-9_\(\_\)\[\]]+	x	x
vmhreaction	[a-zA-Z0-9_\(\_\)\[\]]+	x	x
ocid	ocid:[0-9]{12}	x	x
nemo	[a-z]{3}-[a-km-z0-9]{7}	x	x
minid.test	[A-Za-z0-9]+$	x
transyt	T[A-Z]\d{7}	x	x
knapsack	^C\d{8}		x
biosimulators	[a-zA-Z0-9-_]+	x	x
vmhgene	^[0-9]+\.[0-9]+		x
runbiosimulations	[0-9a-z]{24,24}	x	x

This table was generated with the following python code:

import requests
from tabulate import tabulate

#: see https://docs.identifiers.org/articles/api.html#getdataset
URL = 'https://registry.api.identifiers.org/resolutionApi/getResolverDataset'

def main():
    res = requests.get(URL).json()
    rows = []
    for entry in res['payload']['namespaces']:
        pattern = entry['pattern']
        has_carat = pattern.startswith('^')
        has_dollar = pattern.endswith('$')
        if not has_carat or not has_dollar:
            rows.append((entry['prefix'], pattern, '' if has_carat else 'x', '' if has_dollar else 'x'))
    print(tabulate(rows, headers=['prefix', 'pattern', '^', '$'], tablefmt='html'))

if __name__ == '__main__':
    main()