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[BiONT][BioRDF] Mussels

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 4 May 2006 01:29:42 -0400
Message-Id: <82322AF0-E5F2-42C3-8654-90FBB51DDE44@gmail.com>
Cc: Eric Jain <Eric.Jain@isb-sib.ch>
To: public-semweb-lifesci@w3.org

Here is a typical problem that arises when translating databases. I'm  
reviewing the species that are mentioned as being reactive to various  
of the antibodies in the Alzforum database.

One of them is mussels. Q: what should this resolve to?

I'm looking at the NCBI taxonomy.  There are a bunch of mussels and  
they are not neatly organized:

You can see a number of them at http://www.ebi.ac.uk/newt/display
Search for mussel.

Or you can search for them at NCBI: "*mussel*" and select "wild card"  
from the search pop up.

Here's a list, after I reviewed them quickly to remove things that  
obviously were not mussels (like viruses etc)

Hemistena lata [genbank common name: cracking pearlymussel]
Dromus dromas [genbank common name: dromedary pearlymussel]
Lithophaga nigra [genbank common name: black datemussel]
Musculus discors [genbank common name: discordant mussel]
Hormomya domingensis [genbank common name: Santo Domingo mussel]
Modiolus americanus [genbank common name: American horsemussel]
Musculus lateralis [genbank common name: lateral mussel]
Mytilus californianus [genbank common name: California mussel]
Mytilus edulis [common name: blue mussel]
Mytilus trossulus [genbank common name: common blue mussel]
Sparodon durbanensis [common name: musselcracker seabream]
Lithophaga [genbank common name: date mussels]
Modiolus [genbank common name: horsemussels]
Mytilus galloprovincialis [genbank common name: Mediterranean mussel]
Geukensia demissa [genbank common name: ribbed mussel]
Perna canaliculus [genbank common name: greenshell mussel]
Hormomya exustus [genbank common name: scorched mussel]
Modiolus modiolus [genbank common name: northern horsemussel]
Dreissena bugensis [genbank common name: quagga mussel]
Dreissena polymorpha [common name: zebra mussel]
Mytilopsis leucophaeata [genbank common name: dark false mussel]
Margaritifera margaritifera [genbank common name: freshwater  
pearlshell mussel]
Lexingtonia dolabelloides [common name: slabside pearlymussel]
Lemiox rimosus [common name: birdwing pearly mussel]
Popenaias popeii [common name: Texas hornshell mussel]
Strophitus subvexus [common name: Southern creekmussel]
Venustaconcha pleasii [common name: bleedingtooth mussel]

So there is no single class that will capture all these. Also, most  
likely there is more information that could be gathered from the  
curators, that might narrow this down, but that's certainly  
impractical when automatically translating, and probably impractical  
even when manually annotating.

I can do a further narrowing of the above set by selecting only those  
which are mollusks (though neither newt or the ncbi search box seem  
to provide this ability)

I am inclined to create a class which is the union of all these  
classes and then annotate the antibody with that class.

Anyways, advice about how to handle this case would, I think, carry  
over to many other situations we will hit.

-Alan

ps. for your amusement, here are (most) of the rest of the organisms  
named in this database. Modeling of the terms marked "various" is  
another issue that I need to deal with.


sheep
dog
yeast
mink
mammal (various)
frog
clam
sea star
drosophila
baboon
mussel
coral
goat
fish (various)
zebra
finch
macaque
Dictyostelium
S. pombe
kangaroo
Arabidopsis
microorganism (various)
E. Coli
marsupial
allium
eukaryote
slime molds
plant (various)
nematode
invertebrate (various)
Ascidian
Nicotiana tabacum
trypanosome
syrian hamster
Chlamydomonas reinhardtii
insect
myxo- mycetes
Parasites
ox
alligator
tortoise
opossum
reptile (various)
salamander
donkey
cynomolgus
non-specific
polar bear
torpedo
eel
electrophorus
turtle
bear
ram
fetal calf
rhesus
dolphin
guinea dog
snail
octopus
calf
whale
seal
lamprey
squid
viper
raccoon
mustelid
plasmodium
myxamoeba
eukaryote
african green monkey
kangaroo rat
protozoa
corn (zea mays)
Pisum sativum
wheat
moth
Chlamydomonas
Fungi
dinoflagellate
S. cerevisiae
Arabidopsis thaliana
equine
various animal
chinese hamster
bat
amphibian (various)
sea urchin
goldfish
rodent (various)
ferret
lizard
gerbil
avian (various)
pufferfish
chimpanzee
guinea pig
carp
primate (various)
ovine
various species
C. elegans
various vertebrate
hamster
zebra fish
monkey
bovine
swine
horse
rabbit
porcine
cat
cow
quail
chicken
pig
xenopus
human
rat
mouse
Received on Thursday, 4 May 2006 05:29:55 GMT

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