# [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.