Problems parsing class expressions with object properties in robot templates

[cmungall]

@kaiiam and I are trying to use a template where one of the columns is an expression "RO:nnnnn SOME %". This is failing to parse, as it does not expect SOME. [@kaiiam will update this ticket with specific error messages].

I see from the docs that the default assumption is for a name

If the template string starts with a C and a space then it will be interpreted as a class expression. The value of the current cell will be substituted into the template, replacing all occurrences of the percent % character. Then the result will be parsed into an OWL class expression. ROBOT uses the same syntax for class expressions as Protégé: Manchester Syntax. If it does not recognize a name, ROBOT will assume that you’re trying to refer to a class by its IRI (or compact IRI). This can lead to unexpected behaviour, but it allows you to refer to classes (by IRI) without loading them into the input ontology.

How do we get this parsed as an OP? We tried including -i ro_import.owl but it still seems to assume the RO ID is a class.

Will provide a reproducible example shortly

[kaiiam]

when I try to run it on an example csv file I get the error:

PARSE ERROR error while parsing "RO:0002507 some http://purl.obolibrary.org/obo/ENVO_00000488" at row 3 ("ENVO:3100035"), column 5 ("environmental feature") in table "modules/ebi_biomes.csv": Encountered some at line 1 column 12. Expected one of:
	or
	and
	|EOF|

my csv file is the following:

ID	label	definition	EBI Biomes	environmental feature	environmental material	anatomical entity	quality	biome (subclass of)	EBI Biome Path
ID	LABEL	A IAO:0000115	A http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym	C RO:0002507 some %	C RO:0002507 some %	C RO:0002507 some %	C RO:0000053 some %	C %	A http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
ENVO:3100035	glacial lake biome	A freshwater lake biome which is determined by a glacial lake.	Glacial lake	http://purl.obolibrary.org/obo/ENVO_00000488	http://purl.obolibrary.org/obo/ENVO_01001125			http://purl.obolibrary.org/obo/ENVO_01000252	root > Environmental > Aquatic > Freshwater > Ice > Glacial lake

[cmungall]

Even more minimal example:

foo_template.csv:

ID,P
ID,C RO:1 some C:1
X:1,Y:1

$ robot template -i foo_rel.owl --template foo_template.csv -o z.owl 
PARSE ERROR error while parsing "RO:1 some C:1" at row 3 ("X:1"), column 2 ("P") in table "foo_template.csv": Encountered some at line 1 column 6. Expected one of:
        or
        and
        |EOF|

For details see: http://robot.obolibrary.org/template#parse-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

foo_rel.owl:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/TEMP#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/TEMP"/>
    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_1">
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">foo</rdfs:label>
    </owl:ObjectProperty>
</rdf:RDF>

[cmungall]

AH I SEE, it literally uses the same syntax as Protege, in that the rdfs:label is used (quoted with a space). I wasn't aware that "Protege Manchester Syntax" was a thing as such

[jamesaoverton]

Now I see that there aren't any examples of the interesting Manchester cases in our docs. I'll add an issue for that.

[ramonawalls]

I think my issue is related, but if not, I'm happy to open a new one. I have a template that uses a pattern with two nested SOME statements. Even though the exact same statements exist in our current version of PPO and the same statements work fine when using DOSDP patterns, I get a syntax error from ROBOT when trying to parse the template:

MANCHESTER PARSE ERROR the expression (((OBI:0000293 some PO:0000003) and (OBI:0000299 some (IAO:0000027 and (IAO:0000136 some PPO:0002000))))) at row 7, column 7 in table "../templates/PPO_supporting_classes.tsv" cannot be parsed: encountered unexpected 'some'
	hint: the term before 'some' must be a property

The text version of the above axiom is: ((has specified input some whole plant) and (has specified output some (data item that (is about some plant phenological trait)))

I ran into the same error in another file when I tried to use

PPO:0002001 and (RO:0000080 some (PO:0000003 and (PPO:0000010 some PO:0009011))))

AKA (plant structure presence and (is quality of some (whole plant and (has visible part some plant structure)))

After attempting many permutations, the problem seems to be when using a clause of the form

C and (P some C)

The parser does not properly understand the some.

[jamesaoverton]

The problem is usually that your robot template command needs an --input foo.owl that specifies that P is an object property. And ROBOT is happier using labels in expressions, so it's better to use 'has specified input' (with the single quotes).

[ramonawalls]

Thanks, @jamesaoverton. I tried supplying an input file (I read the robot help page so many times), but could not get it to work. Can you point me at an example?

[matentzn]

@ramonawalls I emailed you just now! If you send me the template I will update the docs / fix the issue in ROBOT!