Large number of duplicated terms

[d0choa]

At least in 3.42 and 3.43, there are a large number of duplicated terms in EFO mostly affecting rare diseases.

Just by lower-casing the names and looking for exact matches, there are 3036 duplicated terms (v3.42). Some of them are explained by disease vs phenotype conondrum, but the vast majority correspond to a MONDO vs Orphanet duplication.

Some examples:

Hemophilia Orphanet:448 - hemophilia MONDO:0018660
Fragile X syndrome Orphanet:908 - fragile X syndrome MONDO:0010383
Apert syndrome Orphanet:87 - apert syndrome MONDO:0007041

...

[zoependlington]

Hi @d0choa, I believe this is due to the gradual replacement of Orphanet terms with Mondo, all of these duplicates will eventually be an obsoleted Orphanet term with a replaced by link to the Mondo term. I will try to prioritise the removal of some of these in time for the July (18th) release.

[zoependlington]

The Orphanet terms have now been obsoleted and replaced with Mondo terms which should now fix this duplication after the July release - please let me know if it persists.

[ireneisdoomed]

I have checked the latest release (3.44.0) and we no longer have Orphanet/MONDO duplication. Thanks @zoependlington!

However, there are still 49 examples with an identical name after converting them to lowercase. Some of them, like arterial occlusion might be coming from the disease vs. phenotype conundrum.

[d0choa]

3 of these have already been fixed in #1698

Many others remain genuine duplications (e.g. polycistic kidney disease)

[zoependlington]

I will add mappings for the following:

http://purl.obolibrary.org/obo/MONDO_0021184	http://www.ebi.ac.uk/efo/EFO_1001303	deltaretrovirus infections	deltaretrovirus infections
http://purl.obolibrary.org/obo/MONDO_0011014	http://www.ebi.ac.uk/efo/EFO_0009052	Pleuropulmonary blastoma	Pleuropulmonary blastoma
http://purl.obolibrary.org/obo/MONDO_0700092	http://www.ebi.ac.uk/efo/EFO_0010642	neurodevelopmental disorder	neurodevelopmental disorder
http://purl.obolibrary.org/obo/MONDO_0012368	http://www.ebi.ac.uk/efo/EFO_1001981	aminoacylase 1 deficiency	aminoacylase 1 deficiency
http://purl.obolibrary.org/obo/MONDO_0020642	http://www.ebi.ac.uk/efo/EFO_0008620	Polycystic Kidney Disease	Polycystic Kidney Disease
http://purl.obolibrary.org/obo/MONDO_0019165	http://www.ebi.ac.uk/efo/EFO_0009029	Central precocious puberty	Central precocious puberty
http://purl.obolibrary.org/obo/MONDO_0014776	http://www.ebi.ac.uk/efo/EFO_0009059	Spinocerebellar ataxia type 42	Spinocerebellar ataxia type 42

The rest have either been taken care of (the measurement terms pointed out above) or are phenotype vs disease.

[zoependlington]

These mappings have now been added so the only duplicates should now be between disease/phenotype terms. Please let me know if that isn't the case.