GSA-GO Linking Summary Tables

Links by GSA Paper ID

110338

GSA Paper ID	Linked Term in Abstract	Linked Term in GO	Instance in Abstract	Synonym match, if applicable	Ontology Aspect (P, F, C)	Larger Phrase in Abstract, if applicable	Best Possible GO Link, if different	Assessment of Existing Link (Y, N, G(ray area))	Comments	Other Actions
110338	male meiosis	GO:0007140 male meiosis	1		P			Y(kv)	missed GO:0007143 female meiosis (kv)
110338	chromosome segregation	GO:0007059 chromosome segregation	1		P	sex chromosome segregation	GO:0016321 female meiosis chromosome segregation, GO:0007060 male meiosis chromosome segregation	Y(kv)	Can we link out to more than one term? (kv)	Ontology development? (kv)
110338	prophase	GO:0051324 prophase	1		P	meiotic prophase	GO:0007128 meiotic prophase I, GO:0007136 meiotic prophase II	Y(kv)	Not clear which meiotic prophase the authors mean and there is no general term for meiotic prophase. (kv)	Add meiotic prophase to GO? (kv)
110338	apoptosis	GO:0006915 apoptosis	1		P	germ-line apoptosis		Y(kv)		Ontology development? - germline vs somatic, if mechanism is different (kv)
110338	signaling	GO:0023052 signaling	1		P	checkpoint signaling	GO:0072411 signal transduction involved in meiotic cell cycle checkpoint	Y(kv)	Maybe even GO:0072461 response to meiotic recombination checkpoint signal
110338	oogenesis	GO:0048477 oogenesis	1		P			Y(kv)
110338	spermatogenesis	GO:0007283 spermatogenesis	1		P			Y(kv)
110338	oogenesis	GO:0048477 oogenesis	2		P			Y(kv)
110338	X chromosome	GO:0000805 X chromosome	1		C			Y(kv)
110338	X chromosome	GO:0000805 X chromosome	2		C			Y(kv)
110338	synapsis	GO:0007129 synapsis	1		P	self-synapsis		Y(kv)		Broaden GO definition? (kv)
110338	apoptosis	GO:0006915 apoptosis	1		P			Y(kv)
110338	chromatin	GO:0000785 chromatin	1		C		GO:0000790 nuclear chromatin	Y(kv)
110338	gene expression	GO:0010467 gene expression	1		P	X-linked gene expression	GO:0009299 mRNA transcription	Y(kv)
110338	chromatin	GO:0000785 chromatin	2		C		GO:0000790 nuclear chromatin	Y(kv)
110338	signaling	GO:0023052 signaling	2		P	checkpoint signaling	GO:0072411 signal transduction involved in meiotic cell cycle checkpoint	Y(kv)	Maybe even GO:0072461 response to meiotic recombination checkpoint signal

123323

GSA Paper ID	Linked Term in Abstract	Linked Term in GO	Instance in Abstract	Synonym match, if applicable	Ontology Aspect (P, F, C)	Larger Phrase in Abstract, if applicable	Best Possible GO Link, if different	Assessment of Existing Link (Y, N, G(ray area))	Comments	Other Actions
123323	diapause	GO:0030431 sleep	1	related	P	entry in the facultative dauer diapause stage	GO:0043053 dauer entry	N(kv)
123323	signaling	GO:0023052 signaling	1		P	DAF-2/Insulin receptor (InsR) signaling	GO:0008286 insulin receptor signaling pathway	Y(kv)	Maybe even GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling
123323	regulation	GO:0065007 biological regulation	1	broad	P	developmental and physiological regulation events	GO:0050793 regulation of developmental process, GO:0050789 regulation of biological process	Y(kv)	regulation of physiological process is an exact synonym for regulation of biological process
123323	signaling	GO:0023052 signaling	2		P	DAF-16/FOXO-dependent branch of the insulin-like signaling	GO:0008286 insulin receptor signaling pathway	Y(kv)	Maybe even GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling
123323	formation	GO:0009058 biosynthetic process	1	exact	P	dauer formation	GO:0043053 dauer entry	N(kv)
123323	insulin-like growth factor	GO:0005159 insulin-like growth factor receptor binding	1	narrow	F	insulin/insulin-like growth factor (IGF)		Y(kv)

123992

GSA Paper ID	Linked Term in Abstract	Linked Term in GO	Instance in Abstract	Synonym match, if applicable	Ontology Aspect (P, F, C)	Larger Phrase in Abstract, if applicable	Best Possible GO Link, if different	Assessment of Existing Link (Y, N, G(ray area))	Comments	Other Actions
123992	cell	GO:0005623 cell	1		C	L3 cell fates		Y(kv)	Link out to life stage for 'L3'? Also, see below.
123992	cell	GO:0005623 cell	2		C	L3 cell fate		Y(kv)	Link out to life stage for 'L3'? Also, see below.
123992	formation	GO:0009058 biosynthetic process	1	exact	P	dauer larva formation	GO:0043053 dauer entry or GO:0040024 dauer larval development	N(kv)
123992	formation	GO:0009058 biosynthetic process	2	exact	P	dauer formation decision	GO:0043053 dauer entry	N(kv))
123992	cell	GO:0005623 cell	3		C	regulate stage-specific cell fate decisions		G(kv)	This link is not incorrect, but like above, 'cell' in this context is part of a larger concept of cell fate specification. There is a GO term, GO:0001708 cell fate specification. Would it be appropriate to link that term instead?
123992	formation	GO:0009058 biosynthetic process	3	exact	P	regulate dauer formation	GO:0043053 dauer entry	N(kv)		Need a new regulation term in GO for dauer entry?

128389

GSA Paper ID	Linked Term in Abstract	Linked Term in GO	Instance in Abstract	Synonym match, if applicable	Ontology Aspect (P, F, C)	Larger Phrase in Abstract, if applicable	Best Possible GO Link, if different	Assessment of Existing Link (Y, N, G(ray area))	Comments	Other Actions
128389	ligand	GO:0005488 binding	1	narrow	F		GO:0005102 receptor binding or GO:0005112 Notch binding	Y(kv)
128389	cell	GO:0005623 cell	1		C	vulval precursor cell (VPC) fate patterning	GO:0072327 vulval cell fate specification	G(kv)	Cell in this context is part of a more specific biological process term.
128389	EGFR	GO:0005006 epidermal growth factor-activated receptor activity	1	exact	F	activation of EGFR/Ras/MAPK by the inductive signal	GO:0035559 MAPKKK cascade involved in epidermal growth factor receptor signaling	G(kv)	Function term contained within a process is the only link; we should link to the process, too. Note also that we could link to GO:0003924 GTPase activity for Ras.
128389	MAPK	GO:0004674 protein serine/threonine kinase activity	1	related	F	activation of EGFR/Ras/MAPK by the inductive signal	GO:0035559 MAPKKK cascade involved in epidermal growth factor receptor signaling	G(kv)	Function term contained within a process is the only link; we should link to the process, too. Note also that we could link to GO:0003924 GTPase activity for Ras.
128389	vulval development	GO:0040025 vulval development	1		P			Y(kv)
128389	signaling	GO:0023052 signaling	1		P	lateral signaling	GO:0046331 lateral inhibition	Y(kv)		Add synonym to GO.
128389	MAPK	GO:0004674 protein serine/threonine kinase activity	2	related	F	MAPK-dependent phosphorylation of LIN-1	GO:0006468 protein phosphorylation	G(kv)	Function term contained within a larger process concept.
128389	phosphorylation	GO:0016310 phosphorylation	1		P	MAPK-dependent phosphorylation of LIN-1	GO:0006468 protein phosphorylation	Y(kv)	Would be best to have the more specific protein phosphorylation term.
128389	transcription	GO:0006351 transcription, DNA-dependent	1	broad	P	transcription of lag-2	GO:0042789 mRNA transcription from RNA polymerase II promoter	Y(kv)

128421

GSA Paper ID	Linked Term in Abstract	Linked Term in GO	Instance in Abstract	Synonym match, if applicable	Ontology Aspect (P, F, C)	Larger Phrase in Abstract, if applicable	Best Possible GO Link, if different	Assessment of Existing Link (Y, N, G(ray area))	Comments	Other Actions
128421	development	GO:0032502 developmental process	1	narrow	P			Y(kv)
128421	cell	GO:0005623 cell	1		C	cell fate		Y(kv)	part of broader concept of cell fate
128421	apoptosis	GO:0006915 apoptosis	1		P			Y(kv)
128421	transcription	GO:0006351 transcription, DNA-dependent	1	broad	P	E2F transcription factors	GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity	N(kv)	The phrase should link out to a function, instead of process, term.
128421	cell cycle	GO:0007049 cell cycle	1		P	regulators of the cell cycle and apoptosis	GO:0051726 regulation of cell cycle ??	Y(kv)
128421	apoptosis	GO:0006915 apoptosis	2		P	regulators of the cell cycle and apoptosis	GO:0042981 regulation of apoptosis ??	Y(kv)
128421	cell	GO:0005623 cell	2		C	cell-type specific context		Y(kv)	part of broader concept
128421	transcription	GO:0006351 transcription, DNA-dependent	2		P	regulate transcription of the egl-1 BH3-only cell death gene	GO:0006357 regulation of transcription from RNA polymerase II promoter	Y(kv)
128421	cell death	GO:0008219 cell death	1		P	egl-1 BH3-only cell death gene		Y(kv)	part of larger concept of cell death gene