EGFR vs epidermal growth factor receptor

[gocentral]

Hello,

Following on from Emilys request to standardise the TGFR/transforming growth factor receptor terms, the same should be done for lots of other signaling terms.

For some the abbreviation is the text string but for others it is the full name. Many are lacking the corresponding synonyms. To be consistent I think the full name should be in the text string and the abbreviation always listed as a synonym.

See:

epidermal growth factor receptor binding ; GO:0005154 epidermal growth factor receptor activating ligand activity ; GO:0005155 epidermal growth factor receptor inhibiting ligand activity ; GO:0005156 vs EGF receptor signaling pathway ; GO:0007173 EGF receptor ligand processing ; GO:0007174 etc

Eph receptor signaling pathway ; GO:0048013 vs ephrin receptor binding ; GO:0046875

hedgehog receptor activity ; GO:0008158 vs activation of hh target transcription factor ; GO:0007228

vascular endothelial growth factor receptor activity ; GO:0005021 vs VEGF receptor signaling pathway ; GO:0048010

Notch binding ; GO:0005112 vs N signaling pathway ; GO:0007219

Toll binding ; GO:0005121 vs Tl signaling pathway ; GO:0008063

fibroblast growth factor receptor activity ; GO:0005007 fibroblast growth factor receptor binding ; GO:0005104 etc vs FGF receptor signaling pathway ; GO:0008543 etc

platelet-derived growth factor receptor activity ; GO:0005017 vs PDGF receptor signaling pathway ; GO:0048008

nerve growth factor receptor binding ; GO:0005163 vs NGF receptor signaling pathway ; GO:0048011

HGF receptor signaling pathway ; GO:0048012 vs hepatocyte growth factor receptor binding ; GO:0005171

IGF receptor signaling pathway ; GO:0048009 vs insulin-like growth factor binding ; GO:0005520 insulin-like growth factor receptor binding ; GO:0005159 insulin-like growth factor receptor activity ; GO:0005010

Need to add: TNF receptor binding/TNF receptor as synonyms for:

tumor necrosis factor receptor binding ; GO:0005164 tumor necrosis factor receptor activity ; GO:0005031

Also, what are:

NGF/TNF (6 C-domain) receptor activity ; GO:0005027 Neu/ErbB-2 receptor binding ; GO:0005176 Neu/ErbB-2 receptor activity ; GO:0005012

they have the distinct hint of geneproduct-ness, or at least 2 separate activities in each term.

Also:

<regulation of signal transduction ; GO:0009966 %negative regulation of signal transduction ; GO:0009968 %positive regulation of signal transduction ; GO:0009967

could be given all the appropriate 'regulation of xxx signaling' children. eg

positive regulation of signal transduction ; GO:0009967 --%positive regulation of FGF receptor signaling pathway ; GO:0045743 etc etc

Thanks, Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/1516":https://sourceforge.net/p/geneontology/ontology-requests/1516

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Standardised term names containing the following so that the full version is in the term name, and the abbreviation is the synonym. Also added synonyms throughout:

EFG -> epidermal growth factor

Eph receptor -> ephrin receptor

VEGF receptor -> vascular endothelial growth factor receptor

N -> Notch

Tl -> Toll

fibroblast growth factor -> FGF

PDGF -> platelet-derived growth factor

nerve growth factor -> NGF

hepatocyte growth factor -> HGF

insulin-like growth factor - > IGF

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

For those 3 terms you mentioned, I suggest:

NGF/TNF (6 C-domain) receptor activity ; GO:0005027 (8 - all TNF receptor) ---%neurotrophin p75 receptor activity ; GO:0005030 (0) ---%tumor necrosis factor receptor activity ; GO:0005031 (25) ------%tumor necrosis factor receptor activity, type I ; GO:0005032 (3) ------%tumor necrosis factor receptor activity, type II ; GO:0005033 (2)

OBSOLETE:

NGF/TNF (6 C-domain) receptor activity ; GO:0005027, suggest -> tumor necrosis factor receptor activity ; GO:0005031

[NGF/TNF (6 C-domain) receptor is a receptor family, not GO activity.]

MERGE:

tumor necrosis factor receptor activity, type I ; GO:0005032 tumor necrosis factor receptor activity, type II ; GO:0005033

into -> tumor necrosis factor receptor activity ; GO:0005031

[type I, II not distinct activities, just different protein structures.]

NEW TERMS:

tumor necrosis factor binding ; GO:new ---%tumor necrosis factor receptor activity ; GO:0005031 (25)

neurotrophin binding ; GO:new ---%neurotrophin receptor activity ; GO:0005030 (NAME CHANGE)

[x receptor activity, where x is a substrate, is_a type of x binding]

Neu/ErbB-2 receptor binding ; GO:0005176 (3 - all Erb) Neu/ErbB-2 receptor activity ; GO:0005012 (2)

SPLIT

Neu/ErbB-2 receptor binding ; GO:0005176 -> ErbB-2 receptor binding ; GO:new, Neu receptor binding ; GO:new

OBSOLETE

Neu/ErbB-2 receptor activity ; GO:0005012 -> ErbB-2 receptor activity ; GO:new, Neu receptor activity ; GO:new

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Added all the appropriate 'regulation of signal transduction ; GO:0009966' parentage.

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Added new term neurotrophin binding (GO:0043121) (as is_a) to growth factor binding (GO:0019838)

Added new term tumor necrosis factor binding (GO:0043120) (as is_a) to cytokine binding (GO:0019955)

Obsoleted tumor necrosis factor receptor activity (GO:0005031) from receptor activity (GO:0004872) with is_a

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Changed the name of 'Neu/ErbB-2 receptor binding ; GO:0005176' -> 'ErbB-2 class receptor binding ; GO:0005176' and added appropriate synonyms.

Obsoleted 'Neu/ErbB-2 receptor activity ; GO:0005012' because it represents a type of receptor rather than an activity.

Replaced with term:

ErbB-3 class receptor binding ; GO:0043125

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Changed the name of 'Neu/ErbB-2 receptor binding ; GO:0005176' -> 'ErbB-2 class receptor binding ; GO:0005176' and added appropriate synonyms.

Obsoleted 'Neu/ErbB-2 receptor activity ; GO:0005012' because it represents a type of receptor rather than an activity.

Replaced with term:

ErbB-3 class receptor binding ; GO:0043125

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242