Today a script from the Bioinformatics world, accessing an EBI REST service called QuickGO, to retrieve Gene Ontology information. For the first script I use the NeoJSON library, and return a Pharo dictionary which we can inspect interactively through the Inspector:
(NeoJSONReader on: (ZnClient new accept: ZnMimeType applicationJson; url: 'http://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0005623,GO:0017071,GO:0030680'; get) readStream) next at: 'results'.
You should only provide the GO identifiers delimited by commas. For the second script we just can join a Collection to build the comma delimited String. The API also includes a service to retrieve a graph image with the terms involved in the query, so we can also try retrieving a different type of information:
| ids |
ids := #('GO:0005623' 'GO:0017071' 'GO:0030680').
(ImageReadWriter formFromStream: (ZnClient new
accept: ZnMimeType imagePng;
url: 'http://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/' , (ids joinUsing: ',') , '/chart';
get) readStream) asMorph openInWindow.
Previously, EBI returned XML content in oboxml format, and the following Pharo script used XML-Parser and XPath (doc) libraries to parse GO terms. I include the script for those discovering Smalltalk and wish to know how it would be using XPath:
#('GO:0005623' 'GO:0017071' 'GO:0030680') collect: [ : goTerm |
| quickGO |
quickGO := 'http://www.ebi.ac.uk/QuickGO-Old/GTerm?id={1}&format=oboxml' format: { goTerm }.
goTerm -> (XPath
for: 'normalize-space(/obo/term/name/text())'
in: (XMLDOMParser on: (ZnEasy get: quickGO) contents) parseDocument) ].
You've got similar code in Perl and Java so you can compare:
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