Difference between revisions of "GSA-GO Linking Summary Tables"

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| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
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|110338||male meiosis||GO:0007140 male meiosis||1||||P||||||Y(kv)||missed GO:0007143 female meiosis (kv); since female meiosis is missed, link to meiosis- not male or female, link not wrong but link should be changed (cg, dr, ky), ok (rk)|||
+
|110338||male meiosis||GO:0007140 male meiosis||1||||P||||||Y(kv); since female meiosis is missed, link to meiosis- not male or female, link not wrong but link should be changed (cg, dr, ky), ok (rk)||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), ok (c,k,r,d)||Can we link out to more than one term? (kv)||Ontology development? (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), ok (c,k,r,d)||Can we link out to more than one term? (kv)||Ontology development? (kv)
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| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|123323||diapause||GO:0030431 sleep||1||related||P||entry in the facultative dauer diapause stage||GO:0043053 dauer entry ||N(kv)|||||
+
|123323||diapause||GO:0030431 sleep||1||related||P||entry in the facultative dauer diapause stage||GO:0043053 dauer entry ||N(kv), N (c,d,r,k)|||||
 
|-
 
|-
−
|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||signaling||GO:0023052 signaling||1||||P||DAF-2/Insulin receptor (InsR) signaling||GO:0008286 insulin receptor signaling pathway||Y(kv); N (c,d,r,k)||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||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); N not specific enough(c,d,r,k)||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||signaling||GO:0023052 signaling||2||||P||DAF-16/FOXO-dependent branch of the insulin-like signaling||GO:0008286 insulin receptor signaling pathway||Y(kv); remove from entity list (c,d,r,k)||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||formation||GO:0009058 biosynthetic process||1||exact||P||dauer formation||GO:0043053 dauer entry||N(kv); remove and link to broader dauer term (c,d,r,k)||||
 
|-
 
|-
−
|123323||insulin-like growth factor||GO:0005159 insulin-like growth factor receptor binding||1||narrow||F||insulin/insulin-like growth factor (IGF)||||Y(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), OK(c, r),(d,k)||||
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===123992===
 
===123992===
Line 93: Line 92:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''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||1||||C||L3 cell fates||||Y(kv); N(c,d,r,k)|||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||cell||GO:0005623 cell||2||||C||L3 cell fate||||Y(kv); N(c,d,r,k)|||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||1||exact||P||dauer larva formation||GO:0043053 dauer entry or GO:0040024 dauer larval development||N(kv); N(c,d,r,k)||||
 
|-
 
|-
−
|123992||formation||GO:0009058 biosynthetic process||2||exact||P||dauer formation decision||GO:0043053 dauer entry||N(kv))||||
+
|123992||formation||GO:0009058 biosynthetic process||2||exact||P||dauer formation decision||GO:0043053 dauer entry||N(kv); (c,d,r,k)||||
 
|-
 
|-
−
|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||cell||GO:0005623 cell||3||||C||regulate stage-specific cell fate decisions||||G(kv); (c,d,r,k)||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?
+
|123992||formation||GO:0009058 biosynthetic process||3||exact||P||regulate dauer formation||GO:0043053 dauer entry||N(kv); (c,d,r,k)|||||Need a new regulation term in GO for dauer entry?
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===128389===
 
===128389===
Line 122: Line 120:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|128389||ligand||GO:0005488 binding||1||narrow||F||||GO:0005102 receptor binding or GO:0005112 Notch binding||Y(kv)|||||
+
|128389||ligand||GO:0005488 binding||1||narrow||F||||GO:0005102 receptor binding or GO:0005112 Notch binding||Y(kv,d);N(c,r,k)|||||
 
|-
 
|-
−
||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||cell||GO:0005623 cell||1||||C||vulval precursor cell (VPC) fate patterning||GO:0072327 vulval cell fate specification||G(kv);N(c,d,r,k)||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||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); Y(c,d,r,k)||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||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); (c,d,r,k)||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||vulval development||GO:0040025 vulval development||1||||P||||||Y(kv); (c,d,r,k)||||
 
|-
 
|-
−
|128389||signaling||GO:0023052 signaling||1||||P||lateral signaling||GO:0046331 lateral inhibition||Y(kv)||||Add synonym to GO.
+
|128389||signaling||GO:0023052 signaling||1||||P||lateral signaling||GO:0046331 lateral inhibition||Y(kv); N(c,d,r,k)||||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||MAPK||GO:0004674 protein serine/threonine kinase activity||2||related||F||MAPK-dependent phosphorylation of LIN-1||GO:0006468 protein phosphorylation||G(kv); Y(c,d,r,k)||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||phosphorylation||GO:0016310 phosphorylation||1||||P||MAPK-dependent phosphorylation of LIN-1||GO:0006468 protein phosphorylation||Y(kv,c,d,r,k)||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)||||
+
|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,c,d,r,k)||||
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===128421===
 
===128421===
Line 157: Line 154:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|128421||development||GO:0032502 developmental process||1||narrow||P||||||Y(kv)|||||
+
|128421||development||GO:0032502 developmental process||1||narrow||P||||||Y(kv,c,d,r,k)|||||
 
|-
 
|-
−
|128421||cell||GO:0005623 cell||1||||C||cell fate||||Y(kv)||part of broader concept of cell fate|||
+
|128421||cell||GO:0005623 cell||1||||C||cell fate||||Y(kv); N(c,d,r,k)||part of broader concept of cell fate|||
 
|-
 
|-
−
|128421||apoptosis||GO:0006915 apoptosis||1||||P||||||Y(kv)|||||
+
|128421||apoptosis||GO:0006915 apoptosis||1||||P||||||Y(kv,c,d,r,k)|||||
 
|-
 
|-
−
|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 AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity||N(kv)||The phrase should link out to a function, instead of process, term.|||
+
|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 AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity||N(kv,c,d,r,k)||The phrase should link out to a function, instead of process, term. Make it a rule to link to transcription factor activity (c,d,r,k).|||
 
|-
 
|-
−
|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||cell cycle||GO:0007049 cell cycle||1||||P||regulators of the cell cycle and apoptosis||GO:0051726 regulation of cell cycle ??||Y(kv,c,d,r,k)|||||
 
|-
 
|-
−
|128421||apoptosis||GO:0006915 apoptosis||2||||P||regulators of the cell cycle and apoptosis||GO:0042981 regulation of apoptosis ??||Y(kv)|||||
+
|128421||apoptosis||GO:0006915 apoptosis||2||||P||regulators of the cell cycle and apoptosis||GO:0042981 regulation of apoptosis ??||Y(kv,c,d,r,k)|||||
 
|-
 
|-
−
|128421||cell||GO:0005623 cell||2||||C||cell-type specific context||||Y(kv)||part of broader concept|||
+
|128421||cell||GO:0005623 cell||2||||C||cell-type specific context||||Y(kv); N(c,d,r,k)||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||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,c,d,r,k)||||
 
|-
 
|-
−
|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||
+
|128421||cell death||GO:0008219 cell death||1||||P||egl-1 BH3-only cell death gene||||Y(kv),c,d,r,k)||part of larger concept of cell death gene||
 
|-
 
|-
−
|128421||cell||GO:0005623 cell||3||||C||to determine cell fate during development||GO:0001709 cell fate determination||N(kv)||cell fate commitment, determination, specification sometimes used interchangeably in C. elegans literature, but GO has specific definitions based on classical embryological expts||
+
|128421||cell||GO:0005623 cell||3||||C||to determine cell fate during development||GO:0001709 cell fate determination||N(kv,c,d,r,k)||cell fate commitment, determination, specification sometimes used interchangeably in C. elegans literature, but GO has specific definitions based on classical embryological expts||
 
|-
 
|-
−
|128421||development||GO:0032502 developmental process||2||narrow||P||||||Y(kv)|||||
+
|128421||development||GO:0032502 developmental process||2||narrow||P||||||Y(kv,c,d,r,k)|||||
 
|}
 
|}
−
 
  
 
===128512===
 
===128512===
Line 195: Line 191:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|128512||receptor||GO:0004872 receptor activity||1||||F||two classes of G protein-coupled receptor (D1-like and D2-like)||GO:0001590 dopamine D1 receptor activity, GO:0001670 dopamine D2 receptor activity||Y(kv)||there is also a parent term of the more specific receptors||Add G protein-coupled receptor activity as a synonym in GO
+
|128512||receptor||GO:0004872 receptor activity||1||||F||two classes of G protein-coupled receptor (D1-like and D2-like)||GO:0001590 dopamine D1 receptor activity, GO:0001670 dopamine D2 receptor activity||Y(kv,c,d,r,k)||there is also a parent term of the more specific receptors||Add G protein-coupled receptor activity as a synonym in GO
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||1||||P||signaling by these coexpressed receptors||GO:0007212 dopamine receptor signaling pathway||Y(kv)||||
+
|128512||signaling||GO:0023052 signaling||1||||P||signaling by these coexpressed receptors||GO:0007212 dopamine receptor signaling pathway||Y(kv); N (c,d,r,k)||||
 
|-
 
|-
−
|128512||motor||GO:0003774 motor activity||1||||F||cholinergic ventral-cord motor neurons||||N(kv)||Best link would be to an anatomy term||
+
|128512||motor||GO:0003774 motor activity||1||||F||cholinergic ventral-cord motor neurons||||N(kv,c,d,r,k)- would be linked to motor neuron wbterm||Best link would be to an anatomy term||
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||2||||P||dopamine signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv)||||
+
|128512||signaling||GO:0023052 signaling||2||||P||dopamine signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv);N(c,d,r,k)||||
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||3||||P||defects in these dopamine-specific behaviors were caused by abnormal signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv)||this might be a stretch||
+
|128512||signaling||GO:0023052 signaling||3||||P||defects in these dopamine-specific behaviors were caused by abnormal signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv); N(c,d,r,k)||this might be a stretch||
 
|-
 
|-
−
|128512||motor||GO:0003774 motor activity||2||||F||cholinergic motor neurons||||N(kv)||Best link would be to an anatomy term||
+
|128512||motor||GO:0003774 motor activity||2||||F||cholinergic motor neurons||||N(kv,c,d,r,k)||Best link would be to an anatomy term||
 
|-
 
|-
−
|128512||motor||GO:0003774 motor activity||3||||F||cholinergic motor neurons||||N(kv)||Best link would be to an anatomy term||
+
|128512||motor||GO:0003774 motor activity||3||||F||cholinergic motor neurons||||N(kv,c,d,r,k)||Best link would be to an anatomy term||
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||4||||P||the sensitivity of dopamine-signaling mutants||GO:0007212 dopamine receptor signaling pathway||Y(kv)||if we were to link to anything here, dopamine signaling seems more appropriate||
+
|128512||signaling||GO:0023052 signaling||4||||P||the sensitivity of dopamine-signaling mutants||GO:0007212 dopamine receptor signaling pathway||Y(kv,c,d,r,k)||if we were to link to anything here, dopamine signaling seems more appropriate||
 
|-
 
|-
−
|128512||acetylcholinesterase||GO:0003990 acetylcholinesterase activity||1||||F||acetylcholinesterase inhibitor aldicarb||||Y(kv)||||Also link out to the molecule?
+
|128512||acetylcholinesterase||GO:0003990 acetylcholinesterase activity||1||||F||acetylcholinesterase inhibitor aldicarb||||Y(kv,c,d,r,k)||||Also link out to the molecule?
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||5||||P||D2 signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv)||||add specific D1 and D2 signaling pathway terms to GO
+
|128512||signaling||GO:0023052 signaling||5||||P||D2 signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv), N(c,d,r,k)||||add specific D1 and D2 signaling pathway terms to GO
 
|-
 
|-
−
|128512||motor||GO:0003774 motor activity||4||||F||cholinergic motor neurons||||N(kv)||Best link would be to an anatomy term||
+
|128512||motor||GO:0003774 motor activity||4||||F||cholinergic motor neurons||||N(kv,c,d,r,k)||Best link would be to an anatomy term||
 
|-
 
|-
−
|128512||signaling||GO:0023052 signaling||6||||P||D1 signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv)||||add specific D1 and D2 signaling pathway terms to GO
+
|128512||signaling||GO:0023052 signaling||6||||P||D1 signaling||GO:0007212 dopamine receptor signaling pathway||Y(kv), N (c,d,r,k)||||add specific D1 and D2 signaling pathway terms to GO
 
|-
 
|-
−
|128512||motor||GO:0003774 motor activity||5||||F||cholinergic motor neurons||||N(kv)||Best link would be to an anatomy term||
+
|128512||motor||GO:0003774 motor activity||5||||F||cholinergic motor neurons||||N(kv); N(c,d,r,k)||Best link would be to an anatomy term||
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===129064===
 
===129064===
Line 238: Line 233:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|129064||gene expression||GO:0010467 gene expression||1||||P||||||Y(kv)||||
+
|129064||gene expression||GO:0010467 gene expression||1||||P||||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129064||gene expression||GO:0010467 gene expression||1||||P||left/right asymmetric gene expression programs of two gustatory neurons||||Y(kv)||||
+
|129064||gene expression||GO:0010467 gene expression||1||||P||left/right asymmetric gene expression programs of two gustatory neurons||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129064||transcription||GO:0006351 transcription, DNA-dependent||1||broad||P||C2H2 zinc-finger transcription factors||GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity||N(kv)||This should link to an MF term.||
+
|129064||transcription||GO:0006351 transcription, DNA-dependent||1||broad||P||C2H2 zinc-finger transcription factors||GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity||N(kv,c,d,r,k)||This should link to an MF term.||
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===129486===
 
===129486===
Line 261: Line 255:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|129486||development||GO:0032502 developmental process||1||narrow||P||animal development||GO:0007275 multicellular organism development||Y(kv)||||
+
|129486||development||GO:0032502 developmental process||1||narrow||P||animal development||GO:0007275 multicellular organism development||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||1||exact||P||morphogenesis genes||||Y(kv)||||
+
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||1||exact||P||morphogenesis genes||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||2||exact||P||morphogenesis mechanisms||||Y(kv)||||
+
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||2||exact||P||morphogenesis mechanisms||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||3||exact||P||an example of morphogenesis||||Y(kv)||||
+
|129486||morphogenesis||GO:0009653 anatomical structure morphogenesis||3||exact||P||an example of morphogenesis||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||gastrulation||GO:0007369 gastrulation||1||||P||an example of morphogenesis, gastrulation||||Y(kv)||||
+
|129486||gastrulation||GO:0007369 gastrulation||1||||P||an example of morphogenesis, gastrulation||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||RNA interference||GO:0016246 RNA interference||1||||P||||||Y(kv)||||
+
|129486||RNA interference||GO:0016246 RNA interference||1||||P||||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||RNAi||GO:0016246 RNA interference||1||exact||P||||||Y(kv)||||
+
|129486||RNAi||GO:0016246 RNA interference||1||exact||P||||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||gastrulation||GO:0007369 gastrulation||2||||P||gastrulation-sensitized double-mutant background||||Y(kv)||||
+
|129486||gastrulation||GO:0007369 gastrulation||2||||P||gastrulation-sensitized double-mutant background||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||gastrulation||GO:0007369 gastrulation||3||||P||normal gastrulation in a nonsensitized background||||Y(kv)||||
+
|129486||gastrulation||GO:0007369 gastrulation||3||||P||normal gastrulation in a nonsensitized background||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||ubiquitin ligase||GO:0004842 ubiquitin-protein ligase activity||1||||F||||||Y(kv)||||
+
|129486||ubiquitin ligase||GO:0004842 ubiquitin-protein ligase activity||1||||F||||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||gastrulation||GO:0007369 gastrulation||4||||P||||||Y(kv)||||
+
|129486||gastrulation||GO:0007369 gastrulation||4||||P||||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|129486||RNAi||GO:0016246 RNA interference||2||exact||P||RNAi-based enhancer screen||||Y(kv)|||
+
|129486||RNAi||GO:0016246 RNA interference||2||exact||P||RNAi-based enhancer screen||||Y(kv,c,d,r,k)|||
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===130450===
 
===130450===
Line 302: Line 295:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|130450||aging||GO:0007568 aging||1||||P||reproductive aging||GO:0010259 multicellular organismal aging||Y(kv)||||Ontology development.
+
|130450||aging||GO:0007568 aging||1||||P||reproductive aging||GO:0010259 multicellular organismal aging||Y(kv,c,d,r), ok but would prefer more specific term(k)||||Ontology development.
 
|-
 
|-
−
|130450||aging||GO:0007568 aging||2||||P||aging of specific somatic tissues||GO:0010259 multicellular organismal aging||Y(kv)||||Ontology development.
+
|130450||aging||GO:0007568 aging||2||||P||aging of specific somatic tissues||GO:0010259 multicellular organismal aging||Y(kv,c,d,r,k), ok but would prefer more specific term(k)||||Ontology development.
 
|-
 
|-
−
|130450||aging||GO:0007568 aging||3||||P||somatic aging||GO:0010259 multicellular organismal aging||Y(kv)||||Ontology development.
+
|130450||aging||GO:0007568 aging||3||||P||somatic aging||GO:0010259 multicellular organismal aging||Y(kv,c,d,r), ok but would prefer more specific term(k)||||Ontology development.
 
|-
 
|-
−
|130450||pharyngeal pumping||GO:0043050 pharyngeal pumping||1||||P||periods of pharyngeal pumping||||Y(kv)||||
+
|130450||pharyngeal pumping||GO:0043050 pharyngeal pumping||1||||P||periods of pharyngeal pumping||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|130450||kinase||GO:0016301 kinase activity||1||||F||phosphatidylinositol-3-kinase||GO:0016303 1-phosphatidylinositol-3-kinase activity||Y(kv)||Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303||Add synonym to GO.
+
|130450||kinase||GO:0016301 kinase activity||1||||F||phosphatidylinositol-3-kinase||GO:0016303 1-phosphatidylinositol-3-kinase activity||Y(kv); N(c,d,r,k):should be linked as PI3K ||Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303||Add synonym to GO.
 
|-
 
|-
−
|130450||PI3K||GO:0016303 1-phosphatidylinositol-3-kinase activity||1||||F||||||Y(kv)||Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303||
+
|130450||PI3K||GO:0016303 1-phosphatidylinositol-3-kinase activity||1||||F||||||Y(kv,c,d,r,k)||Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303||
 
|-
 
|-
−
|130450||insulin-like growth factor||GO:0005159 insulin-like growth factor receptor binding||1||||F||insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway||GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling||N(kv)||This links to a function term, but the larger phrase should link to the process term.|||
+
|130450||insulin-like growth factor||GO:0005159 insulin-like growth factor receptor binding||1||||F||insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway||GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling||N(kv);G(d,k);Y(c,r)||This links to a function term, but the larger phrase should link to the process term.|||
 
|-
 
|-
−
|130450||signaling pathway||GO:0007165 signal transduction||1||related||P||insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway||GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling||Y(kv)|||||
+
|130450||signaling pathway||GO:0007165 signal transduction||1||related||P||insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway||GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling||Y(kv,c,d); G but remove in this context(r); N(k)|||||
 
|-
 
|-
−
|130450||pharyngeal pumping||GO:0043050 pharyngeal pumping||2||||P||extensions of the pharyngeal pumping and body movement spans||||Y(kv)||||
+
|130450||pharyngeal pumping||GO:0043050 pharyngeal pumping||2||||P||extensions of the pharyngeal pumping and body movement spans||||Y(kv,c,d,r,k)||||
 
|-
 
|-
−
|130450||aging||GO:0007568 aging||4||||P||reproductive aging||GO:0010259 multicellular organismal aging||Y(kv)||||Ontology development.
+
|130450||aging||GO:0007568 aging||4||||P||reproductive aging||GO:0010259 multicellular organismal aging||Y(kv,c,d,r), ok but would prefer more specific term(k)||||Ontology development.
 
|-
 
|-
−
|130450||regulation||GO:0065007 biological regulation||1||broad||P||genetic regulation of age-related degenerative changes in somatic and reproductive tissues||GO:0050789 regulation of biological process||Y(kv)||||Needs ontology development.
+
|130450||regulation||GO:0065007 biological regulation||1||broad||P||genetic regulation of age-related degenerative changes in somatic and reproductive tissues||GO:0050789 regulation of biological process||Y(kv); remove regulation from the entity list it is too general of a term(c,r,d,k)||||Needs ontology development.
 
|-
 
|-
 
|}
 
|}
−
 
  
 
===131227===
 
===131227===
Line 341: Line 333:
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Other Actions'''
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||1||exact||F||||||Y(kv)||||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||1||exact||F||||||Y(kv);N, the first RhoGEF is fine, we would remove all links to it when it is part of a specific protein(c,r,d,k)||||
 
|-
 
|-
−
|131227||axon guidance||GO:0007411 axon guidance||1||||P||||||Y(kv)||||
+
|131227||axon guidance||GO:0007411 axon guidance||1||||P||||||Y(kv,c,r,k,d)||||
 
|-
 
|-
−
|131227||cell migration||GO:0016477 cell migration||1||||P||||||Y(kv)||||
+
|131227||cell migration||GO:0016477 cell migration||1||||P||||||Y(kv,c,r,k,d)||||
 
|-
 
|-
−
|131227||phagocytosis||GO:0006909 phagocytosis||1||||P||||||Y(kv)||||
+
|131227||phagocytosis||GO:0006909 phagocytosis||1||||P||||||Y(kv,c,r,k,d)||||
 
|-
 
|-
−
|131227||neurotransmission||GO:0007268 synaptic transmission||1||related||P||||||Y(kv)||||
+
|131227||neurotransmission||GO:0007268 synaptic transmission||1||related||P||||||Y(kv,c,r,k,d)||||
 
|-
 
|-
−
|131227||GTPase||GO:0003924 GTPase activity||1||||F||Rac or Rho GTPase subfamilies||||Y(kv)||Note that Rho small monomeric GTPase activity is a narrow synonym, but Rac is not.||Add Rac as a narrow synonym.
+
|131227||GTPase||GO:0003924 GTPase activity||1||||F||Rac or Rho GTPase subfamilies||||Y(kv,c,r,k,d); need to add plural form||Note that Rho small monomeric GTPase activity is a narrow synonym, but Rac is not.||Add Rac as a narrow synonym.
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||2||exact||F||a Rac-specific RhoGEF-1 domain||||Y(kv)||What about linking out to InterPro or Pfam protein domain databases?||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||2||exact||F||a Rac-specific RhoGEF-1 domain||||Y(kv), see notes above||What about linking out to InterPro or Pfam protein domain databases?||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||3||exact||F||a Rho-specific RhoGEF-2 domain||||Y(kv)||What about linking out to InterPro or Pfam protein domain databases?||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||3||exact||F||a Rho-specific RhoGEF-2 domain||||Y(kv), see notes above||What about linking out to InterPro or Pfam protein domain databases?||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||4||exact||F||RhoGEF-2 isoform||||Y(kv)||||
+
|131227||RhoGEF, see notes above||GO:0005089 Rho guanyl-nucleotide exchange factor activity||4||exact||F||RhoGEF-2 isoform||||Y(kv)||||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||5||exact||F||RhoGEF-2 isoform||||Y(kv)||||
+
|131227||RhoGEF, see notes above||GO:0005089 Rho guanyl-nucleotide exchange factor activity||5||exact||F||RhoGEF-2 isoform||||Y(kv)||||
 
|-
 
|-
−
|131227||locomotion||GO:0040011 locomotion||1||||P||normal rates of locomotion||||Y(kv)||||
+
|131227||locomotion||GO:0040011 locomotion||1||||P||normal rates of locomotion||||Y(kv,c,r,d,k)||||
 
|-
 
|-
−
|131227||regulation of locomotion||GO:0040012 regulation of locomotion||1||||P||||||Y(kv)||||
+
|131227||regulation of locomotion||GO:0040012 regulation of locomotion||1||||P||||||Y(kv,c,r,d,k)||||
 
|-
 
|-
−
|131227||regulation||GO:0065007 biological regulation||1||broad||P||regulation of motility||GO:0040012 regulation of locomotion||Y(kv)||||Add as synonym of regulation of locomotion.
+
|131227||regulation||GO:0065007 biological regulation||1||broad||P||regulation of motility||GO:0040012 regulation of locomotion||Y(kv); delete from entity list (c,d,r,k)||||Add as synonym of regulation of locomotion.
 
|-
 
|-
−
|131227||cell||GO:0005623 cell||1||||C||cell-specific and inducible promoters|||||Y(kv)||||
+
|131227||cell||GO:0005623 cell||1||||C||cell-specific and inducible promoters|||||Y(kv); N (c,r,d,k)||||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||6||exact||F||RhoGEF-2 isoform||||Y(kv)||||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||6||exact||F||RhoGEF-2 isoform||||Y(kv), see notes above (c,r,d,k)||||
 
|-
 
|-
−
|131227||locomotion||GO:GO:0040011 locomotion||2||||P||regulate locomotion rate||GO:0040012 regulation of locomotion||Y(kv)||||Add synonym?
+
|131227||locomotion||GO:GO:0040011 locomotion||2||||P||regulate locomotion rate||GO:0040012 regulation of locomotion||Y(kv,c,r,d,k)||||Add synonym?
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||7||exact||F||RhoGEF-2 mutants||||Y(kv)||||
+
|131227||RhoGEF, see notes above (c,r,d,k)||GO:0005089 Rho guanyl-nucleotide exchange factor activity||7||exact||F||RhoGEF-2 mutants||||Y(kv)||||
 
|-
 
|-
−
|131227||acetylcholinesterase||GO:0003990 acetylcholinesterase activity||1||||F||acetylcholinesterase inhibitor aldicarb||||Y(kv)||Link out to molecule, also?||
+
|131227||acetylcholinesterase||GO:0003990 acetylcholinesterase activity||1||||F||acetylcholinesterase inhibitor aldicarb||||Y(kv,c,r,d,k)||Link out to molecule, also?||
 
|-
 
|-
−
|131227||acetylcholine receptor||GO:0015464 acetylcholine receptor activity||1||||F||acetylcholine receptor agonist levamisole||||Y(kv)||Link out to molecule, also?||
+
|131227||acetylcholine receptor||GO:0015464 acetylcholine receptor activity||1||||F||acetylcholine receptor agonist levamisole||||Y(kv,c,r,d,k)||Link out to molecule, also?||
 
|-
 
|-
−
|131227||signaling||GO:0023052 signaling||1||||P||acetylcholine neurotransmitter signaling||GO:0007271 synaptic transmission, cholinergic||||Y(kv)||
+
|131227||signaling||GO:0023052 signaling||1||||P||acetylcholine neurotransmitter signaling||GO:0007271 synaptic transmission, cholinergic||||Y(kv); remove from entity list (c,d,r,k)||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||8||exact||F||RhoGEF-2 mutants||||Y(kv)||||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||8||exact||F||RhoGEF-2 mutants||||Y(kv), see notes above (c,r,d,k)||||
 
|-
 
|-
−
|131227||motor||GO:0003774 motor activity||1||||F||motor neuron dense core vesicles (DCVs)||||N(kv)||Eliminate link to motor if followed by neuron or neurons.||
+
|131227||motor||GO:0003774 motor activity||1||||F||motor neuron dense core vesicles (DCVs)||||N(kv); would be linked to wb motor neuron term||Eliminate link to motor if followed by neuron or neurons.||
 
|-
 
|-
−
|131227||signaling||GO:0023052 signaling||2||||P||DCV-mediated signaling defects||GO:0007268 synaptic transmission||Y(kv)||||
+
|131227||signaling||GO:0023052 signaling||2||||P||DCV-mediated signaling defects||GO:0007268 synaptic transmission||Y(kv); remove from entity list(c,r,d,k)||||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||9||exact||F||RhoGEF-2 and rab-2 lethargic movement phenotypes||||Y(kv)||||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||9||exact||F||RhoGEF-2 and rab-2 lethargic movement phenotypes||||Y(kv), see notes above(c,r,d,k)||||
 
|-
 
|-
−
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||10||exact||F||RhoGEF-2 isoforms||||Y(kv)||||
+
|131227||RhoGEF||GO:0005089 Rho guanyl-nucleotide exchange factor activity||10||exact||F||RhoGEF-2 isoforms||||Y(kv), see notes above(c,r,d,k)||||
 
|-
 
|-
−
|131227||signaling||GO:0023052 signaling||3||||P||neurotransmitter signaling||GO:0007268 synaptic transmission||Y(kv)||||Add synonym to GO?
+
|131227||signaling||GO:0023052 signaling||3||||P||neurotransmitter signaling||GO:0007268 synaptic transmission||Y(kv); remove from entity list (c,r,d,k)||||Add synonym to GO?
 
|-
 
|-
−
|131227||regulation of locomotion||GO:0040012 regulation of locomotion||2||||P||DCV-mediated neuromodulatory regulation of locomotion rate||||Y(kv)||||
+
|131227||regulation of locomotion||GO:0040012 regulation of locomotion||2||||P||DCV-mediated neuromodulatory regulation of locomotion rate||||Y(kv,c,d,r,k)||||
 
|-
 
|-
 
|}
 
|}

Latest revision as of 18:16, 21 September 2011

Back to GO entity markup

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); since female meiosis is missed, link to meiosis- not male or female, link not wrong but link should be changed (cg, dr, ky), ok (rk) 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), ok (c,k,r,d) 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), fine (c,k,r,d) 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), fine (all) 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), No (all), this term needs to be removed from the list Maybe even GO:0072461 response to meiotic recombination checkpoint signal
110338 oogenesis GO:0048477 oogenesis 1 P Y(kv)(all)
110338 spermatogenesis GO:0007283 spermatogenesis 1 P Y(kv)(all)
110338 oogenesis GO:0048477 oogenesis 2 P Y(kv)(all)
110338 X chromosome GO:0000805 X chromosome 1 C Y(kv)(all) need to add plural form to entity lists(cg)
110338 X chromosome GO:0000805 X chromosome 2 C Y(kv)(all)
110338 synapsis GO:0007129 synapsis 1 P self-synapsis Y(kv)(all) Broaden GO definition? (kv)
110338 apoptosis GO:0006915 apoptosis 1 P Y(kv)(all)
110338 chromatin GO:0000785 chromatin 1 C GO:0000790 nuclear chromatin Y(kv)(all)
110338 gene expression GO:0010467 gene expression 1 P X-linked gene expression GO:0009299 mRNA transcription Y(kv)(all)
110338 chromatin GO:0000785 chromatin 2 C GO:0000790 nuclear chromatin Y(kv)(all)
110338 signaling GO:0023052 signaling 2 P checkpoint signaling GO:0072411 signal transduction involved in meiotic cell cycle checkpoint Y(kv); get rid of(all) 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), N (c,d,r,k)
123323 signaling GO:0023052 signaling 1 P DAF-2/Insulin receptor (InsR) signaling GO:0008286 insulin receptor signaling pathway Y(kv); N (c,d,r,k) 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); N not specific enough(c,d,r,k) 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); remove from entity list (c,d,r,k) 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); remove and link to broader dauer term (c,d,r,k)
123323 insulin-like growth factor GO:0005159 insulin-like growth factor receptor binding 1 narrow F insulin/insulin-like growth factor (IGF) Y(kv), OK(c, r),(d,k)

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); N(c,d,r,k) Link out to life stage for 'L3'? Also, see below.
123992 cell GO:0005623 cell 2 C L3 cell fate Y(kv); N(c,d,r,k) 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); N(c,d,r,k)
123992 formation GO:0009058 biosynthetic process 2 exact P dauer formation decision GO:0043053 dauer entry N(kv); (c,d,r,k)
123992 cell GO:0005623 cell 3 C regulate stage-specific cell fate decisions G(kv); (c,d,r,k) 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); (c,d,r,k) 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,d);N(c,r,k)
128389 cell GO:0005623 cell 1 C vulval precursor cell (VPC) fate patterning GO:0072327 vulval cell fate specification G(kv);N(c,d,r,k) 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); Y(c,d,r,k) 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); (c,d,r,k) 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); (c,d,r,k)
128389 signaling GO:0023052 signaling 1 P lateral signaling GO:0046331 lateral inhibition Y(kv); N(c,d,r,k) 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); Y(c,d,r,k) 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,c,d,r,k) 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,c,d,r,k)

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,c,d,r,k)
128421 cell GO:0005623 cell 1 C cell fate Y(kv); N(c,d,r,k) part of broader concept of cell fate
128421 apoptosis GO:0006915 apoptosis 1 P Y(kv,c,d,r,k)
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 AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity N(kv,c,d,r,k) The phrase should link out to a function, instead of process, term. Make it a rule to link to transcription factor activity (c,d,r,k).
128421 cell cycle GO:0007049 cell cycle 1 P regulators of the cell cycle and apoptosis GO:0051726 regulation of cell cycle ?? Y(kv,c,d,r,k)
128421 apoptosis GO:0006915 apoptosis 2 P regulators of the cell cycle and apoptosis GO:0042981 regulation of apoptosis ?? Y(kv,c,d,r,k)
128421 cell GO:0005623 cell 2 C cell-type specific context Y(kv); N(c,d,r,k) 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,c,d,r,k)
128421 cell death GO:0008219 cell death 1 P egl-1 BH3-only cell death gene Y(kv),c,d,r,k) part of larger concept of cell death gene
128421 cell GO:0005623 cell 3 C to determine cell fate during development GO:0001709 cell fate determination N(kv,c,d,r,k) cell fate commitment, determination, specification sometimes used interchangeably in C. elegans literature, but GO has specific definitions based on classical embryological expts
128421 development GO:0032502 developmental process 2 narrow P Y(kv,c,d,r,k)

128512

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
128512 receptor GO:0004872 receptor activity 1 F two classes of G protein-coupled receptor (D1-like and D2-like) GO:0001590 dopamine D1 receptor activity, GO:0001670 dopamine D2 receptor activity Y(kv,c,d,r,k) there is also a parent term of the more specific receptors Add G protein-coupled receptor activity as a synonym in GO
128512 signaling GO:0023052 signaling 1 P signaling by these coexpressed receptors GO:0007212 dopamine receptor signaling pathway Y(kv); N (c,d,r,k)
128512 motor GO:0003774 motor activity 1 F cholinergic ventral-cord motor neurons N(kv,c,d,r,k)- would be linked to motor neuron wbterm Best link would be to an anatomy term
128512 signaling GO:0023052 signaling 2 P dopamine signaling GO:0007212 dopamine receptor signaling pathway Y(kv);N(c,d,r,k)
128512 signaling GO:0023052 signaling 3 P defects in these dopamine-specific behaviors were caused by abnormal signaling GO:0007212 dopamine receptor signaling pathway Y(kv); N(c,d,r,k) this might be a stretch
128512 motor GO:0003774 motor activity 2 F cholinergic motor neurons N(kv,c,d,r,k) Best link would be to an anatomy term
128512 motor GO:0003774 motor activity 3 F cholinergic motor neurons N(kv,c,d,r,k) Best link would be to an anatomy term
128512 signaling GO:0023052 signaling 4 P the sensitivity of dopamine-signaling mutants GO:0007212 dopamine receptor signaling pathway Y(kv,c,d,r,k) if we were to link to anything here, dopamine signaling seems more appropriate
128512 acetylcholinesterase GO:0003990 acetylcholinesterase activity 1 F acetylcholinesterase inhibitor aldicarb Y(kv,c,d,r,k) Also link out to the molecule?
128512 signaling GO:0023052 signaling 5 P D2 signaling GO:0007212 dopamine receptor signaling pathway Y(kv), N(c,d,r,k) add specific D1 and D2 signaling pathway terms to GO
128512 motor GO:0003774 motor activity 4 F cholinergic motor neurons N(kv,c,d,r,k) Best link would be to an anatomy term
128512 signaling GO:0023052 signaling 6 P D1 signaling GO:0007212 dopamine receptor signaling pathway Y(kv), N (c,d,r,k) add specific D1 and D2 signaling pathway terms to GO
128512 motor GO:0003774 motor activity 5 F cholinergic motor neurons N(kv); N(c,d,r,k) Best link would be to an anatomy term

129064

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
129064 gene expression GO:0010467 gene expression 1 P Y(kv,c,d,r,k)
129064 gene expression GO:0010467 gene expression 1 P left/right asymmetric gene expression programs of two gustatory neurons Y(kv,c,d,r,k)
129064 transcription GO:0006351 transcription, DNA-dependent 1 broad P C2H2 zinc-finger transcription factors GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity AND GO:0001076 RNA polymerase II transcription factor binding transcription factor activity N(kv,c,d,r,k) This should link to an MF term.

129486

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
129486 development GO:0032502 developmental process 1 narrow P animal development GO:0007275 multicellular organism development Y(kv,c,d,r,k)
129486 morphogenesis GO:0009653 anatomical structure morphogenesis 1 exact P morphogenesis genes Y(kv,c,d,r,k)
129486 morphogenesis GO:0009653 anatomical structure morphogenesis 2 exact P morphogenesis mechanisms Y(kv,c,d,r,k)
129486 morphogenesis GO:0009653 anatomical structure morphogenesis 3 exact P an example of morphogenesis Y(kv,c,d,r,k)
129486 gastrulation GO:0007369 gastrulation 1 P an example of morphogenesis, gastrulation Y(kv,c,d,r,k)
129486 RNA interference GO:0016246 RNA interference 1 P Y(kv,c,d,r,k)
129486 RNAi GO:0016246 RNA interference 1 exact P Y(kv,c,d,r,k)
129486 gastrulation GO:0007369 gastrulation 2 P gastrulation-sensitized double-mutant background Y(kv,c,d,r,k)
129486 gastrulation GO:0007369 gastrulation 3 P normal gastrulation in a nonsensitized background Y(kv,c,d,r,k)
129486 ubiquitin ligase GO:0004842 ubiquitin-protein ligase activity 1 F Y(kv,c,d,r,k)
129486 gastrulation GO:0007369 gastrulation 4 P Y(kv,c,d,r,k)
129486 RNAi GO:0016246 RNA interference 2 exact P RNAi-based enhancer screen Y(kv,c,d,r,k)

130450

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
130450 aging GO:0007568 aging 1 P reproductive aging GO:0010259 multicellular organismal aging Y(kv,c,d,r), ok but would prefer more specific term(k) Ontology development.
130450 aging GO:0007568 aging 2 P aging of specific somatic tissues GO:0010259 multicellular organismal aging Y(kv,c,d,r,k), ok but would prefer more specific term(k) Ontology development.
130450 aging GO:0007568 aging 3 P somatic aging GO:0010259 multicellular organismal aging Y(kv,c,d,r), ok but would prefer more specific term(k) Ontology development.
130450 pharyngeal pumping GO:0043050 pharyngeal pumping 1 P periods of pharyngeal pumping Y(kv,c,d,r,k)
130450 kinase GO:0016301 kinase activity 1 F phosphatidylinositol-3-kinase GO:0016303 1-phosphatidylinositol-3-kinase activity Y(kv); N(c,d,r,k):should be linked as PI3K Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303 Add synonym to GO.
130450 PI3K GO:0016303 1-phosphatidylinositol-3-kinase activity 1 F Y(kv,c,d,r,k) Note that GO has a parent term GO:0035004 phosphatidylinositol 3-kinase activity, but that PI3K is an exact synonym of GO:0016303
130450 insulin-like growth factor GO:0005159 insulin-like growth factor receptor binding 1 F insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling N(kv);G(d,k);Y(c,r) This links to a function term, but the larger phrase should link to the process term.
130450 signaling pathway GO:0007165 signal transduction 1 related P insulin/insulin-like growth factor-1 (IGF-1) signaling pathway OR phosphatidylinositol-3-kinase (PI3K) that functions in the insulin/insulin-like growth factor-1 (IGF-1) signaling pathway GO:0008286 insulin receptor signaling pathway OR GO:0035558 phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling Y(kv,c,d); G but remove in this context(r); N(k)
130450 pharyngeal pumping GO:0043050 pharyngeal pumping 2 P extensions of the pharyngeal pumping and body movement spans Y(kv,c,d,r,k)
130450 aging GO:0007568 aging 4 P reproductive aging GO:0010259 multicellular organismal aging Y(kv,c,d,r), ok but would prefer more specific term(k) Ontology development.
130450 regulation GO:0065007 biological regulation 1 broad P genetic regulation of age-related degenerative changes in somatic and reproductive tissues GO:0050789 regulation of biological process Y(kv); remove regulation from the entity list it is too general of a term(c,r,d,k) Needs ontology development.

131227

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
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 1 exact F Y(kv);N, the first RhoGEF is fine, we would remove all links to it when it is part of a specific protein(c,r,d,k)
131227 axon guidance GO:0007411 axon guidance 1 P Y(kv,c,r,k,d)
131227 cell migration GO:0016477 cell migration 1 P Y(kv,c,r,k,d)
131227 phagocytosis GO:0006909 phagocytosis 1 P Y(kv,c,r,k,d)
131227 neurotransmission GO:0007268 synaptic transmission 1 related P Y(kv,c,r,k,d)
131227 GTPase GO:0003924 GTPase activity 1 F Rac or Rho GTPase subfamilies Y(kv,c,r,k,d); need to add plural form Note that Rho small monomeric GTPase activity is a narrow synonym, but Rac is not. Add Rac as a narrow synonym.
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 2 exact F a Rac-specific RhoGEF-1 domain Y(kv), see notes above What about linking out to InterPro or Pfam protein domain databases?
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 3 exact F a Rho-specific RhoGEF-2 domain Y(kv), see notes above What about linking out to InterPro or Pfam protein domain databases?
131227 RhoGEF, see notes above GO:0005089 Rho guanyl-nucleotide exchange factor activity 4 exact F RhoGEF-2 isoform Y(kv)
131227 RhoGEF, see notes above GO:0005089 Rho guanyl-nucleotide exchange factor activity 5 exact F RhoGEF-2 isoform Y(kv)
131227 locomotion GO:0040011 locomotion 1 P normal rates of locomotion Y(kv,c,r,d,k)
131227 regulation of locomotion GO:0040012 regulation of locomotion 1 P Y(kv,c,r,d,k)
131227 regulation GO:0065007 biological regulation 1 broad P regulation of motility GO:0040012 regulation of locomotion Y(kv); delete from entity list (c,d,r,k) Add as synonym of regulation of locomotion.
131227 cell GO:0005623 cell 1 C cell-specific and inducible promoters Y(kv); N (c,r,d,k)
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 6 exact F RhoGEF-2 isoform Y(kv), see notes above (c,r,d,k)
131227 locomotion GO:GO:0040011 locomotion 2 P regulate locomotion rate GO:0040012 regulation of locomotion Y(kv,c,r,d,k) Add synonym?
131227 RhoGEF, see notes above (c,r,d,k) GO:0005089 Rho guanyl-nucleotide exchange factor activity 7 exact F RhoGEF-2 mutants Y(kv)
131227 acetylcholinesterase GO:0003990 acetylcholinesterase activity 1 F acetylcholinesterase inhibitor aldicarb Y(kv,c,r,d,k) Link out to molecule, also?
131227 acetylcholine receptor GO:0015464 acetylcholine receptor activity 1 F acetylcholine receptor agonist levamisole Y(kv,c,r,d,k) Link out to molecule, also?
131227 signaling GO:0023052 signaling 1 P acetylcholine neurotransmitter signaling GO:0007271 synaptic transmission, cholinergic Y(kv); remove from entity list (c,d,r,k)
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 8 exact F RhoGEF-2 mutants Y(kv), see notes above (c,r,d,k)
131227 motor GO:0003774 motor activity 1 F motor neuron dense core vesicles (DCVs) N(kv); would be linked to wb motor neuron term Eliminate link to motor if followed by neuron or neurons.
131227 signaling GO:0023052 signaling 2 P DCV-mediated signaling defects GO:0007268 synaptic transmission Y(kv); remove from entity list(c,r,d,k)
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 9 exact F RhoGEF-2 and rab-2 lethargic movement phenotypes Y(kv), see notes above(c,r,d,k)
131227 RhoGEF GO:0005089 Rho guanyl-nucleotide exchange factor activity 10 exact F RhoGEF-2 isoforms Y(kv), see notes above(c,r,d,k)
131227 signaling GO:0023052 signaling 3 P neurotransmitter signaling GO:0007268 synaptic transmission Y(kv); remove from entity list (c,r,d,k) Add synonym to GO?
131227 regulation of locomotion GO:0040012 regulation of locomotion 2 P DCV-mediated neuromodulatory regulation of locomotion rate Y(kv,c,d,r,k)


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