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# [gn-transform-databases/ADR-001] Remodel GeneRIF_BASIC (NCBI RIFs) Metadata Using predicateObject Lists
* author: bonfacem
* status: rejected
* reviewed-by: pjotr, jnduli
## Context
We can model RIF comments using pridacetobject lists as described in:
=> https://issues.genenetwork.org/topics/ADR/gn-transform-databases/000-remodel-rif-transform-with-predicateobject-lists [ADR/gn-transform-databases] Remodel GeneRIF Metadata Using predicateObject Lists
However, currently for NCBI RIFs we represent comments as blank nodes:
```
gn:symbolsspA rdfs:comment [
rdf:type gnc:NCBIWikiEntry ;
rdfs:comment "N-terminus verified by Edman degradation on mature peptide"^^xsd:string ;
gnt:belongsToSpecies gn:Mus_musculus ;
skos:notation taxon:511145 ;
gnt:hasGeneId generif:944744 ;
dct:hasVersion '1'^^xsd:int ;
dct:references pubmed:97295 ;
...
dct:references pubmed:15361618 ;
dct:created "2007-11-06T00:38:00"^^xsd:datetime ;
] .
gn:symbolaraC rdfs:comment [
rdf:type gnc:NCBIWikiEntry ;
rdfs:comment "N-terminus verified by Edman degradation on mature peptide"^^xsd:string ;
gnt:belongsToSpecies gn:Mus_musculus ;
skos:notation taxon:511145 ;
gnt:hasGeneId generif:944780 ;
dct:hasVersion '1'^^xsd:int ;
dct:references pubmed:320034 ;
...
dct:references pubmed:16369539 ;
dct:created "2007-11-06T00:39:00"^^xsd:datetime ;
] .
```
Here we see alot of duplicated entries for the same symbols. For the above 2 entries, everything is exactly the same except for the "gnt:hasGeneId" and "dct:references" predicates.
## Decision
We use predicateObjectLists with blankNodePropertyLists as an idiom to represent the generif comments.
=> https://www.w3.org/TR/turtle/#grammar-production-predicateObjectList predicateObjectList
=> https://www.w3.org/TR/turtle/#grammar-production-blankNodePropertyList blankNodePropertyList
In so doing, we can de-duplicate the entries demonstrated above. A representation of the above RDF Turtle triples would be:
```
[ rdfs:comment "N-terminus verified by Edman degradation on mature peptide"^^xsd:string ]
rdf:type gnc:NCBIWikiEntry ;
dct:created "2007-11-06T00:39:00"^^xsd:datetime ;
gnt:belongsToSpecies gn:Mus_musculus ;
skos:notation taxon:511145 ;
dct:hasVersion '1'^^xsd:int ;
rdfs:seeAlso [
gnt:hasGeneId generif:944744 ;
gnt:symbol gn:symbolsspA ;
dct:references ( pubmed:97295 ... pubmed:15361618 ) ;
] ;
rdfs:seeAlso [
gnt:hasGeneId generif:944780 ;
gn:symbolaraC ;
dct:references ( pubmed:320034 ... pubmed:16369539 ) ;
] .
```
The above would translate to the following triples:
```
_:comment rdfs:comment "N-terminus verified by Edman degradation on mature peptide"^^xsd:string .
_:comment rdfs:type gn:NCBIWikiEntry .
_:comment dct:created "2007-11-06T00:39:00"^^xsd:datetime .
_:comment gnt:belongsToSpecies gn:Mus_musculus .
_:comment skos:notation taxon:511145 .
_:comment dct:hasVersion '1'^^xsd:int .
_:comment rdfs:seeAlso _:metadata1
_:comment rdfs:seeAlso _:metadata2 .
_:metadata1 gnt:hasGeneId generif:944744 .
_:metadata1 gnt:symbol gn:symbolaraC .
_:metadata1 dct:references ( pubmed:97295 ... pubmed:15361618 )
_:metadata2 gnt:hasGeneId generif:944780 .
_:metadata2 gnt:symbol gn:symbolsspA .
_:metadata2 dct:references ( pubmed:320034 ... pubmed:16369539 ) .
```
Beyond that, we intentionally use a sequence to store a list of pubmed references.
## Consequences
* De-duplication of comments during the transform while retaining the integrity of the RIF metadata.
* Because of the terseness, less work during the I/O heavy operation.
* Update SPARQL in tux02, tux01 in lockstep with updating GN3/GN2 and the XAPIAN index.
## Rejection Rationale
This proposal was rejected because relying on blank-nodes as an identifier is opaque and not human-readable. We want to use human readable identifiers where possible.
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