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Table 3 Recursive syntactic rules order, constituent terms, and example generated synonyms

From: Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition

Order

Rule

GO term

Constituent terms

Generated synonyms

1

“via” or “involved in” terms

GO:0002679 - respiratory burst involved in defense response

“respiratory burst”, “defense response”

“defense response associated respiratory burst”

2

“regulation of” terms

GO:0030513 - positive regulation of BMP signaling pathway

“BMP signaling pathway”

‘positive regulation of BMP receptor pathway”, “up-regulation of BMP receptor signaling”

3

“response to” terms

GO:0034263 - autophagy in response to ER overload

“autophagy”, “ER overload”

“ER overload responsible for autophagy”, “autophagy response to ER overload”

4

“signaling” terms

GO:0035329 - hippo signaling

“hippo”

“hippo signaling pathway”, “signaling of hippo”

5

“biosynthetic process” terms

GO:0042095 - interferon-gamma biosynthetic process

“interferon-gama”

“interferon-gamma biosynthesis”, “production of interferon-gamma”

6

“metabolic process” terms

GO:0042120 - alginic acid metabolic process

“alginic acid”

“metabolism of alginic acid”, “alginic acid metabolism”

7

“catabolic process” terms

GO:0042190 - vanillin catabolic process

“vanillin”

“vanillin degradation”, “breakdown of vanillin”

8

“binding” terms

GO:0042314 - bacteriochlorophyll binding

“bacteriochlorophyll”

“binding of bacteriochlorophyll”, “bacteriochlorophyll bound”

9

“transport” terms

GO:0042876 - aldarate transmembrane transporter activity

“aldarate”, “transmembrane”

“transportation of aldarate across the membrane”, “transporting aldarate transmembrane”

10

“differentiation” terms

GO:0043158 - heterocyst differentiation

“heterocyst”

“heterocyst cell differentiation”, “differentiation into heterocyst”

11

“activity” terms

GO:0043492 - ATPase activity, coupled to movement of substances

“ATPase”, “coupled to movement of substances”

“ATPase, coupled to movement of substances”, “coupled to movement of substances activity of ATPase”

  1. While these examples show only one rule applied at once, each constituent term identified recursively goes through each rule in the order outlined to determine the most basic constituent terms, which will get derivational variations (discussed in next paragraph) and then combinatorially re-combined into generated synonyms of the original term