updated docs

misc-scripts/xref_mapping/parsing_information.txt

@@ -28,11 +28,6 @@ This is a list of dependent Xrefs that might be added:
     EMBL
     PDB
     protein_id
-    GO
-    MIM_GENE     (human only)
-    MIM_MORBID   (human only)
-    HUGO         (human only)
-    MarkerSymbol (mouse only) aka MGI.
 
 
 Refseq_peptide
@@ -54,10 +49,7 @@ Exonerate).
 
 Below is a list of dependent Xrefs that might be added:
 
-    GO
     EntrezGene
-    HUGO (human only)
-    RGD (rat only)
 
 
 Refseq_dna
@@ -77,10 +69,6 @@ These are primary Xrefs in that they contain sequence and hence can be
 mapped to the Ensembl entities via normal alignment methods (we use
 Exonerate).
 
-Below is a list of dependent Xrefs that might be added:
-
-    HUGO (human only)
-    RGD  (rat only)
 
 
 IPI (International Protein Index)
@@ -276,25 +264,44 @@ So when the Swissprot entries are matched to Ensembl the MIM entries
 will also be matched.
 
 
-HUGO
+HGNC
 ----
 
-The Human Genome Organisation Xrefs are obtained from using the
-following URL:
+The Human Genome Organisation Xrefs are obtained from three files
+
+These are 
+1) HUGO_TO_ENSG
+   a local file which has a list of HGNC, ensembl gene pairs. (Direct xrefs)
+This is made from the Havana manually curated database.
 
-http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl?title=Genew+output+data
+2) CCDS_TO_HUGO
+  a local file which has a list of CCDS, HGNC pairs. (Direct xrefs)
+The HGNC's are connected to the same ensembl object that the CCDS are linked 
+to.
+
+3) Downloaded via the url:-
+http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data
 &col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases
-&col=md_prot_id&col=gd_pub_refseq_ids&status=Approved&status=Approved+Non-Human
-&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit
-&.cgifields=&.cgifields=status&.cgifields=chr
+&col=md_prot_id&col=gd_pub_refseq_ids&col=md_eg_id&status=Approved
+&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id
+&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
 
-Which is a script that produces a list of HUGO identifiers with the
+Which is a script that produces a list of HGNC identifiers with the
 UniProt and RefSeq entries they are linked to.
 
-The files have references to UniProt and RefSeq entries and so the GO
+The files have references to UniProt and RefSeq entries and so the HGNC
 entries are set to be dependent Xref on these.
 
-NOTE:  This data will be stored as the file 'gdlw.pl'.
+
+
+Which of these is chosen at the mapping stage is based on the prioritys of 
+the sources. Here they are listed in order so if a HGNC can be assigned via 
+HUGO_TO_ENSG (1) then the other two sources will be ignored.
+
+This is known as a priority xref as the mapping with the best priority is 
+chosen.  
+
+
 
 
 OTTT