Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait

BMC Plant Biology

Table 1 Sets representing first order (direct) neighbors of flesh color nodes. Set A represents first-order neighbors of tuber flesh color nodes found in full-text articles. Set B represents first-order neighbors of tuber flesh color nodes found in abstracts of articles of the training set. The difference between these sets (SET A - SET B) represents all entities that are first-order neighbors of tuber flesh color in full-text articles, but not in abstracts alone

Set A	Set B	Set A - Set B
AN1	anthocyanin	AN1
anthocyanidin	ascorbic acid	anthocyanidin
anthocyanin	b-carotene	carotene hydroxylase
ascorbic acid	b-carotene hydroxylase	cyanidin
b-carotene	bHLH	epoxides
b-carotene hydroxylase	caffeic acid	essential amino acids
bHLH	carotenoid	glycosides
caffeic acid	CCD	lutein
carotene hydroxylase	chlorogenic acid	lutein-5,6-epoxide
carotenoid	CHY	malvidin
CCD	Or	nonepoxide
chlorogenic acid	phenolic	pelargonidin
CHY	TP	peonidin
cyanidin	tuberigen activation complex	petunidin
epoxides	xanthophyll	Pf
essential amino acids	zeaxanthin	phenolic acid
glycosides	zeaxanthin epoxidase	phytoene synthase
lutein		polyphenol
lutein-5,6-epoxide		recessiveZEP
malvidin		violaxanthin
nonepoxide		violaxanthin-like carotenoid
Or
pelargonidin
peonidin
petunidin
Pf
phenolic
phenolic acid
phytoene synthase
polyphenol
recessiveZEP
TP
tuberigen activation complex
violaxanthin
violaxanthin-like carotenoid
xanthophyll
zeaxanthin
zeaxanthin epoxidase

ISSN: 1471-2229