Do not delete.

Queries

SPECIES:
	chebi:
		for ~ http://identifiers.org/chebi/CHEBI:15905

		<annotation>
          <rdf:RDF>
            <rdf:Description rdf:about="#meta_s_0017">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15905"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>


		SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'chebi' AND d.id = s.data_source_id AND s.synonym = 'CHEBI:37637' AND s.ome_id = c.id;

	kegg.compound:d
		for ~ http://identifiers.org/kegg.compound/C03492


		<annotation>
          <rdf:RDF>
            <rdf:Description rdf:about="#meta_s_0017">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15905"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C03492"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>

        SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'kegg.compound' AND d.id = s.data_source_id AND s.synonym = 'C03492' AND s.ome_id = c.id;

  hmdb:
    http://identifiers.org/hmdb/HMDB62758

	SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'hmdb' AND d.id = s.data_source_id AND s.synonym = 'HMDB62758' AND s.ome_id = c.id;

  mnx.chemical:
  	- change metanetx.chemical = mnx.chemical
	
    SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'mnx.chemical' AND d.id = s.data_source_id AND s.synonym = 'MNXM275' AND s.ome_id = c.id;

  lipidmaps:
    SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'lipidmaps' AND d.id = s.data_source_id AND s.synonym = 'LMFA01010002' AND s.ome_id = c.id;

  kegg.drug:
    SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'kegg.drug' AND d.id = s.data_source_id AND s.synonym = 'D00010' AND s.ome_id = c.id;

  seed.compound
    "http://identifiers.org/seed.compound/cpd00482"

    SELECT c.bigg_id FROM component c, data_source d, synonym s WHERE d.bigg_id = 'seed.compound' AND d.id = s.data_source_id AND s.synonym = 'cpd00482' AND s.ome_id = c.id;



  biocyc:
    http://identifiers.org/biocyc/META:2-PG

        
  sgd:
  	"http://identifiers.org/sgd/S000007283"

  	Abv query didn't work as S000007283 is a gene 
  	Also even if we map to gene -> the gene table does not have bigg_id

  	ONLY THESE HAVE bigg_id column:
		 data_source
		 model
		 reaction
		 compartment
		 component
		 genome_region

  uniprot:
    found in yeast
      "http://identifiers.org/uniprot/P22217"
      -P should be cropped
      -its also a gene so cannot give a biggid


                
		

REACTIONS: 
	similar for kegg.reactions

  mnx.equation:
    http://identifiers.org/metanetx.reaction/MNXR95210
    - need to convert metanetx.reaction -> mnx.equation
    - evth else fine

    SELECT r.bigg_id FROM reaction r, data_source d, synonym s WHERE d.bigg_id = 'mnx.equation' AND d.id = s.data_source_id AND s.synonym = 'MNXR95210' AND s.ome_id = r.id;

  ec:
    http://identifiers.org/ec-code/2.7.2.1
    - need to convert ec-code to ec
    - else fine

    SELECT r.bigg_id FROM reaction r, data_source d, synonym s WHERE d.bigg_id = 'ec' AND d.id = s.data_source_id AND s.synonym = '2.7.2.1' AND s.ome_id = r.id;

  rhea:
    http://identifiers.org/rhea/11352
    -evth fine
    SELECT r.bigg_id FROM reaction r, data_source d, synonym s WHERE d.bigg_id = 'rhea' AND d.id = s.data_source_id AND s.synonym = '11352' AND s.ome_id = r.id;

GENE PRODUCT (yeast)
  
  gi:
	  All synonym in synonym table for http://identifiers.org/ncbigi/gi: are of format 'numeric'
		  Will need to check if 'gi:' present then remove it

  goa:
    <rdf:li rdf:resource="http://identifiers.org/goa/B7M6M3" />
    Found in a polished model
    No problem with the synonym or bigg id of datasource but it gives a gene

  interpro:
    "http://identifiers.org/interpro/IPR016038"
    Correct synonym and data_source id but its again a gene so no bigg_id and multiple entries in synonym table with same synonym id

  asap:, ncbigene:, ecogene:
    http://identifiers.org/asap/ABE-0012215
    "http://identifiers.org/ncbigene/948254"
    "http://identifiers.org/ecogene/EG10106"
    Correct synonym and data_source id but its again a gene    

COMPARTMENT
	**Same as above for go, also note obo.go but big_id is go
		http://identifiers.org/obo.go/GO:0005794"
		Need to remove 'go:00' as all synonym are 5 digit





NOT FOUND
- pdb
- ccds
- omim
- hprd
- reactome