Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/16

Hi,

For the keyword mapping I would like a GO term
to use for proteins involved in the formation/development
of a fruiting body. My also need a component term?
Not affecting many proteins.

Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/35

Hi,

May I please have the new child terms
of interferon-gamma biosynthesis GO:GO:0042095
(which BTW needs its synonym updated from INF to IFN :-))
regulation of interferon-gamma biosynthesis
inhibition of interferon-gamma biosynthesis
activation of interferon-gamma biosynthesis

Regulation, activation and inhibition is probably needed
for all cytokine biosynthesis terms when added.

oh the joy:
Evelyn

The above needed for GO annotation of: P29460

Reported by: nobody

Original Ticket: geneontology/ontology-requests/48

Hi

Please remove cytokine from under growth factor term
in the function ontology. There is now the support
of at least 4 immunologists…

cheers
Evelyn

>ISSUE:
>
>[i] growth factor (GO:0008083)
> [i] cytokine (GO:0005125)
> i] hematopoeitin/interferon-class (D200-domain) cytokine
>receptor ligand
> (GO:0005126)
> [i] erythropoietin receptor ligand (GO:0005128)
> [i] granulocyte-macrophage colony stimulating factor receptor
> ligand (GO:0005129)
>
>Hi,
>
>Currently the ‘cytokine’ GO term is under ‘growth factor’.
>My view is that not all cytokines are growth factors.
>
>The ones that are include:
>
>Interleukin receptor ligands..
>Colony-Stimulating Factors receptor ligands
>Stem Cell Factor receptor ligand
>
>The cytokines that are not growth factors include:
>
>Interferon receptor ligand
>chemokines?

Reported by: nobody

Original Ticket: geneontology/ontology-requests/37

Hi,

Please add new GO term for:
acetylcholine binding
SWISS-PROT AC:Q9GZZ6
EV CODE:TAS

cheers
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/41

Hi,

Currently SWISS-PROT keyword ‘RNA repair’ is mapped to
RNA ligase (GO:0008452). There are only 4 SP entries
withthis keyword and they are all RNA ligases so for the
moment this mapping is semi-OK. But if we have
DNA repair perhaps a new term for ‘RNA repair’ is required.

KEYWORD DEF:
ID RNA repair.
DE Protein involved in the repair of RNA, the various biochemical
DE processes by which damaged RNA can be restored.

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/32

Hi,

Just came across and noticed there was not a general
term.
Might need more research:

http://axon.bhs.mq.edu.au/PSY\804/Lecture\_2/Lecture\2.html

Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/39

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/9

Hi,

I have discussed this with Kathy (incyte) can you
please considering copying the term ‘neutrophil activation’
and ‘macrophage activation’ as a child of ‘inflammatory response’
as well as ‘immune response’.

cheers
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/47

Evelyn asked for this a while ago, so I’m putting it in the tracker:

Q9H254: clustering of voltage-gated sodium channels

It will require more generic terms, such as "ion channel clustering," as parents.

midori

Reported by: mah11

Original Ticket: geneontology/ontology-requests/40

Hi,

Reminder: we need to resolve how to refer to
the function of blocking a cytokine binding to its receptor.
Is the blocker a ‘receptor inhibitor’ or an ‘antagonist’
or both? Should we say ‘antagonist to Interleukin-8 binding’
or ‘Interleukin-8 receptor antagonist’ or ‘Interleukin-8 antagonist’.
Not fond of ‘Interleukin-8 receptor inhibitor’ as the molecule
which may block IL-8 binding to its receptor may still transduce
a weak signal through the IL-8 receptor, therefore not entirely
inhibiting IL-8 receptor function..
‘interleukin-1 receptor antagonist’ is a nice existing example
which is a child of ‘interleukin-1 receptor ligand’

cheers
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/46

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/4

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/21

I was just wondering if it is necessary to keep
antibacterial humoral response 19731 as a child of
antimicrobial humoral response (sensu Vertebrata) 19735
since the more specific term:antibacterial humoral
response (sensu Vertebrata) 19733 is also a child of
19731 above. Same question re: antifungal humoral
response 19732

Here is this part of the hierarchy:

antimicrobial humoral response (sensu Vertebrata) 19735
antibacterial humoral response 19731
antibacterial humoral response (sensu
Vertebrata) 19733
antifungal humoral response 19732
antifungal humoral response (sensu
Vertebrata) 19734

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/26

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/22

Evelyn Camon has requested ‘RPTP-like protein binding’; I’m testing this system.
-midori

Reported by: mah11

Original Ticket: geneontology/ontology-requests/1

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/10

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/18

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/5

Hi,

Midori mentioned might be made obsolete.
As used in keyword2go mapping I need to
monitor.

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/34

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/6

Hi,

Please move ‘interleukin-8 receptor ligand’ GO:0005153
to be a child of chemokine instead of cytokine…
or create another child under chemokine…
P10145

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/42

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/23

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/8

Hi,

Explanation: NK (natural killer) cells identify targets cells
for lysing by the level of MHC-class I expressed on their surface.
Cells with low levels of MHC-class I undergo
NK-cell mediated lysis.

For annotation of MHC-class I can I have the new terms:
‘susceptibility to cytolysis’ or
‘protection from NK-mediated cytolysis’

cheers big ears!
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/49

Hi,

From my discussions with Katy (Incyte) we
request the following new terms (indicated by *).

[i] cell differentiation (GO:0030154)
[i] lymphocytic blood cell differentiation (GO:0030098)
T cell selection*
thymic T cell selection*
positive T cell selection*
negative T cell selection*
extrathymic T cell selection*
positive T cell selection*
negative T cell selection*

[i] cell differentiation (GO:0030154)
[i] lymphocytic blood cell differentiation (GO:0030098)
[i] T-cell differentiation (GO:0030217)
T helper cell (Th0) differentiation
Th1 cell differentiation*
Th2 cell differentiation*
Cytotoxic T cell differentiation*
Suppressor T cell differentiation* (?)

On the topic of hemopoiesis, it isn’t really the correct term for T (effector) cell
differentiation but it won’t do too much harm to have T cell differentiation there
since they are obviously trying to communicate the
developmental process that leads up to immune cells which circulate in
blood, which T cells do.

Might get back to this discussion later, but if you could add
T selection terms that would be great to distinquish hemopoiesis
in the thymus.

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/36

term: phosphatidyl transferase
definition: A reaction involving the transfer of a
phosphatidate
(diacylglycerol 3-phosphosphate) moiety.
reference: Sanger:MB

1. parent

A good parent would be "transferase, transferring
hosphorus-containing groups (GO:0016772)"

1. child

"cardiolipin synthase (GO:0008808) "

Reported by: mberriman

Original Ticket: geneontology/ontology-requests/30

Hi,

You have the GO term:chemoattractant (GO:0042056)
may I have neutrophil chemoattractant? perhaps
you don’t want to go that far…

Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/44

Hi,

Please add as children to Interleukin-12 receptor ligand:
GO:0005143

interleukin-12 beta-1 receptor ligand (synonym:IL-12RB1 ligand, IL-12R-beta1)
interleukin-12 beta-2 receptor ligand (synonym:IL-12RB2 ligand, IL-12R-beta2)
(When I am annotating IL-12p40 I would like to indicate
which part of the receptor it is a ligand for)

Please add as children to Interleukin-12 binding:GO:0019972

interleukin-12 alpha subunit binding (synonym IL-12A, IL-12p35, CLMFp40, NKSFp35)
interleukin-12 beta subunit binding (synonym IL-12B, IL-12p40, CLMFp40, NKSFp40)

(p40 and p35 bind to each other)

thats all
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/38

Hi,

Needed for keyword mapping.
Midori already aware…added to Soureforge so I
can monitor.

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/33

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/12

should "chromosome organization and biogenesis ;
GO:0007001" be a parent of "establishment and/or
maintenance of chromatin architecture ; GO:0006325"?

Reported by: mberriman

Original Ticket: geneontology/ontology-requests/29

The term attenuation of antimicrobial humoral
response⁸³⁴⁸ is currently a parent of antifungal
humoral response (sensu Invertebrata)⁶⁹⁶⁶
Could this be included as a child of :
antibacterial humoral response (sensu Invertebrata)
(6961) and the corresponding vertebrate terms: (19731)
and (19732)?
Thanks!
Lisa

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/27

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/17

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/3

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/11

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/15

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/19

Hi,

May I have a new term:
regulation of viral genome replication
as a child of GO:0019079.

You may also need positive/negative regulation?

SWISS-PROT:P10145
PUBMED:11483765

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/45

Hi,

This new term ‘collagen catabolism’
is needed for spkw mapping to collagen degradation.

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/31

‘Gene silencing’ (GO:0016458) has some parents that lead to non-True Paths. Move it and create children to deal with the stress and defense response connections.

Reported by: mah11

Original Ticket: geneontology/ontology-requests/24

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/13

Hi,

Please consider new term:

‘C-X-C chemokine receptor binding’

needed for IL-8 annotation

thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/43

Hi,

Can we please have ‘innate immune response’
(synonym: non-specific immune response)
as a new term and child of ‘immune response’:
GO:0006955.
Innate immune response is very important first line of defense.
It can also activate the adaptive immune response via
inflammation as a danger signal that something has damaged the
host tissue.

Also can I have ‘regulation of the innate immune response’,
‘activation of the innate immune response’
(eg. for annotation of Toll receptors in Drosophila)

Then make ‘inflammatory response’, GO:0006954,
‘activation of natural killer cell activity’,
GO:0030101, ‘macrophage activation’ GO:0006955,
neutrophil activation,GO:0042119
a child of ‘innate immune response’.
others may follow ……

please and thankyou…

cheers
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/50

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/14

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/7

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/20

The term regulator of G protein signaling ¹⁶²⁹⁹ should
come out from under the parent term small GTPase
regulatory/interacting protein, since many if not most
Regulator of G protein signaling proteins interact with
heterotrimeric G proteins (which are not usually called
small GTPases).

regulator of G-protein signaling¹⁶²⁹⁹
small GTPase regulatory/interacting protein⁵⁰⁸³
receptor signaling protein⁵⁰⁵⁷
signal transducer⁴⁸⁷¹
molecular_function³⁶⁷⁴

Suggest bringing it up to be a sibling term of small
GTPase regulatory/interacting protein⁵⁰⁸³

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/25

Hi,

Please consider new terms for Cnidocyst:SWISSPROT: P01533
This is a new SWISS-PROT Keyword

SPKW DEFINITION:
ID Cnidocyst.
DE Protein localized in the cnidocyst, an organelle found in cnidoblast
DE (nematoblast) cells. When matured, these stinging organelles store
DE toxins and can deliver them when the cnidocil (a short extension of
DE the cnidocyst) is stimulated by a prey or another stimulus. These
DE proteins are principally found in anemones.
SY Nematocyst.
RU CC-SUBCELLULAR LOCATION: Cnidocyst and then secreted.

many thanks
Evelyn

Reported by: nobody

Original Ticket: geneontology/ontology-requests/28

Reported by: lmatthews

Original Ticket: geneontology/ontology-requests/2