dosumis
commented
7 years ago Some concerns:
New schema is slightly denormalized for data_source linkouts. It requires two edges for every individual linked rather than one. I'll stick to this plan for now, but for maintenance purposes, it would be better if this representation was prod only.
Make sites for each resource
- FlyCircuit
MATCH (ds:data_source { name: 'Chiang2010' })
MERGE (s:Site { label : "FlyCircuit" })
SET s.link_base = ds.data_link_pre
SET s.iri = "http://flycircuit.tw"
REMOVE ds.data_link_pre
MERGE (s)<-[:has_site]-(ds)- [x] Tested
- [x] Implemented
- FlyLight
MATCH (ds:data_source { name: 'Jenett2012' })
MERGE (s:Site { label : "FlyLight" })
SET s.link_base = ds.data_link_pre
SET s.iri = "http://flweb.janelia.org/cgi-bin/flew.cgi"
SET s.logo_url = "http://flweb.janelia.org/images/fly_light_color.png"
REMOVE ds.data_link_pre
MERGE (s)<-[:has_site]-(ds)- [x] Tested
- [x] Implemented
- BrainTrap
MATCH (ds:data_source { name: 'Knowles-Barley2010'})
MERGE (s:Site { label : "BrainTrap"})
SET s.link_base = ds.data_link_pre
REMOVE ds.data_link_pre
SET s.iri = "http://braintrap.inf.ed.ac.uk/braintrap/"
SET s.logo_url = "http://braintrap.inf.ed.ac.uk/braintrap/images/BrainTrap-bg1.gif"
MERGE (s)<-[:has_site]-(ds)- [x] Tested
- [x] Implemented
- [ ] LMB NBLAST Clusters
CREATE (s:site { label : "Jefferis lab - NBLAST Neuron clusters: ",
iri: "http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/" // doesn't resolve
link_base: "http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/" })
MERGE (s)<-[:has_site]-(ds:data_source { name: 'CostaJefferis2010' })Accession for these will be {cluster version number}/exemplar}
- [ ] Jefferis lab - NBLAST on-the-fly
Create edge from all FlyCircuit neurons for these ?
CREATE (:site { label : "NBLAST on-the-fly: Neurons" ,
iri: "http://flybrain.mrc-lmb.cam.ac.uk:8080/NBLAST_on-the-fly"
link_base : 'http://flybrain.mrc-lmb.cam.ac.uk:8080/NBLAST_on-the-fly/?all_query="'
link_postfix : '&all_use_mean=TRUE'})
CREATE (:site { label : "Jefferis lab - NBLAST on-the-fly: GAL4",
iri: "http://flybrain.mrc-lmb.cam.ac.uk:8080/NBLAST_on-the-fly/?all_query=&all_use_mean=F&gal4_n=10&gal4_query=&tab=One%20against%20all"
link_base = 'http://flybrain.mrc-lmb.cam.ac.uk:8080/NBLAST_on-the-fly/?gal4_query=',
link_postfix : '"&tab=GAL4"' })Move accessions to ds-site edges
MATCH (s:Site)-[:has_site]-(ds:data_source)<-[hs:has_source]-(i:Individual)
MERGE (i)-[dbx:hasDbXref]-(s) SET dbx.accession = hs.id_in_source
REMOVE hs.id_in_source - [x] Tested
- [x] Implemented
Generic mechanism for expanding xrefs on classes in ontology to linkouts:
xref strings are {DB}:{accession} A lookup for dbs can be found ind
site.xref_db = {DB} hasDbXref.accession = {accession}
Cypher for generating these in prod.
OLS neo pre-parses:
annotation-database_cross_reference: [VFB:FBbt_00007263] obo_xref:[{"database":"VFB","id":"FBbt_00007263","description":null,"url":null}]
obo_xref is a list of JSON strings - not (unfortunately) a cypher map. So processing either will require some scripting.
MATCH (s:Site) ASSERT s.xref_db IS UNIQUE
MATCH (c:Class) WHERE exists(c.obo_xref) RETURN c.short_form as class_sfid, c.obo_xref as class_xrefs
MATCH (s:Site) WHERE exists(s.xref_db) RETURN map( s.xref_db -> s.iri)Iterate over class - xref -> Iterate over xrefs -> convert each to json, check if j['database] in c.obo_xref
-> roll cypher
Other sites for linkouts:
-
[ ] FlyBrain NDB Links from Classes Drop this?? given it will be shut down soon?
MERGE (s:Site { label: "FlyBrain NeuronDB" ) SET s = { label: "FlyBrain NeuronDB", iri : "http://flybrain-ndb.iam.u-tokyo.ac.jp/", link_icon_url : "http://flybrain-ndb.iam.u-tokyo.ac.jp/NDB_title260.gif", link_base: "http://flybrain-ndb.iam.u-tokyo.ac.jp/fmi/xsl/browserecord.xsl?-lay=NDB&Accession+number=", link_postfix: "&-find=-find" }- [x] Tested
- [x] Implemented
-
[ ] NeuroLex Links from classes (expand from DBxref) Drop this?
-
[ ] Fruit Fly Brain Observatory Links from Inds. No link recipe yet.
-
[ ] DoOR Links from classes - Need to be added to Ontology.
MERGE (s:Site { label: 'DoOR' })
SET s.description = "Database of Odorant responses."
SET s.iri = "http://neuro.uni-konstanz.de/DoOR"
SET s.xref_db = "DoOR"
SET s.link_base = "http://neuro.uni-konstanz.de/DoOR/content/receptor.php?OR="
SET s.link_icon_url = 'http://neuro.uni-konstanz.de/DoOR/navi_pic.jpg' - [x] Tested
- [x] Implemented
- [ ] Insect Brain DB Links from classes for Neuropils - (But note have more detailed semantics for links.
- [x] FlyBase Note: We currently roll all these simply by making the URLs of entities = link.
MERGE (s:Site { label: "FlyBase"})
SET s.iri = "http://flybase.org"
SET s.link_base = "http://flybase.org/reports"
SET s.link_icon_url = "http://flybase.org/static_pages/images/global/fly_logo.png"
SET s.description = "A Database of Drosophila Genes & Genomes."- [x] Tested
- [x] Implemented
Need consistency with spec here: https://github.com/VirtualFlyBrain/VFB_neo4j/blob/master/src/uk/ac/ebi/vfb/neo4j/flybase2neo/import_all_pub_data.py#L47
-
[ ] Bloomington Stock Center
-
[ ] VDRC
mmc46
Currently:
(Individual)-[:has_source { ID_in_source: 'fubar' })-(:data_source { data_link_pre: ''...})
Switch to
Generic linkouts (NEO only):
(n)-[hasDBxref { accession : '' }]->(s:site { link_base: '', URI: '', name: '', png_path: '' })
data_source (NEO only):
(:Individual:anat)-[:has_data_source]-(:data_source)
(:Individual:anat)-[:hasDBxref { accession : '', is_source = True }]-(s:site)
(ds:data_source)-[:has_reference]-(p:Pub)
(ds)-[:has_site]-(s)
(ds)-[:has_license]-(:License)