Category:RefGenome Electronic Jamboree 2009-07 SLC11A1/2

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See the talk page for discussion. See also Help:Annotation Jamborees

Orthoset

Participants

Name	Group	Organism(s)/Genome(s)	Notes
Rob Nash	SGD	S. cerevisiae
Stan Laulederkind	RGD	Rat
Petra Fey	dictyBase	D. discoideum
Pascale Gaudet	dictyBase	D. discoideum
Li Ni	MGI	Mouse	Slc11a1=MGI:1345275=UniProtKB:P41251 Slc11a2=MGI:1345279=UniProtKB:P49282
Dmitry Sitnikov	MGI	Mouse	Slc11a1=MGI:1345275=UniProtKB:P41251
Susan Tweedie	flyBase	D. melanogaster
Brenley McIntosh	ecoliwiki	E. coli	ECOLI:mntH (P0A769)
Jodi Hirschman	SGD	S. cerevisiae
Emily Dimmer	GOA	Human
Yasmin Alam-Faruque	GOA	Human
Rachael Huntley	GOA	Human
Varsha Khodiyar	BHF-UCL	Human
Ruth Lovering	BHF-UCL	Human
Debby Siegele	ecoliwiki	E. coli	ECOLI:mntH (P0A769)
Kimberly Van Auken	WormBase	C. elegans	smf-1=WBGene00004876, smf-2=WBGene00004877, smf-3=WBGene00004878
Ranjana Kishore	WormBase	C. elegans	smf-1=WBGene00004876, smf-2=WBGene00004877, smf-3=WBGene00004878
Lakshmi Pillai	AgBase	G. gallus
Tanya Berardini	TAIR	A. thaliana
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Annotations

Aspect	ID	Term	CHICK B3F8C5	CHICK B3F8C6	TAIR AT1G15960.1	TAIR AT1G47240.1	TAIR AT1G80830.1	TAIR AT2G23150.1	TAIR AT4G18790.1	TAIR AT5G67330.1	WB smf‑1	WB smf‑2	WB smf‑3	ZFIN slc11a2	dictyBase nramp1	FB Mvl	ECOLI mntH	CHICK NRAM1	CHICK Q0GMA8	HUMAN NRAM1	HUMAN NRAM2	HUMAN Q8IUD7	MGI Slc11a1	MGI Slc11a2	RAT NRAM1	RAT NRAM2	SGD SMF1	SGD SMF2	SGD SMF3	SCHPO PDT1
Biological Process	GO:0000041	transition metal ion transport									ISS	ISS	ISS			IMP								ISO		IDA
Biological Process	GO:0000060	protein import into nucleus, translocation																					IMP
Biological Process	GO:0000165	MAPKKK cascade																					ISO
Biological Process	GO:0001666	response to hypoxia																			IEP	IEP
Biological Process	GO:0001818	negative regulation of cytokine production																		ISS			IMP
Biological Process	GO:0001819	positive regulation of cytokine production																		ISS			IMP
Biological Process	GO:0002309	T cell proliferation involved in immune response																		ISS			IMP
Biological Process	GO:0002369	T cell cytokine production																		ISS			IMP
Biological Process	GO:0002606	positive regulation of dendritic cell antigen processing and presentation																		ISS			IMP
Biological Process	GO:0002827	positive regulation of T-helper 1 type immune response																		ISS			IMP
Biological Process	GO:0003032	detection of oxygen																			IEP NOT IEP	IEP NOT IEP
Biological Process	GO:0006778	porphyrin-containing compound metabolic process																						IMP
Biological Process	GO:0006779	porphyrin-containing compound biosynthetic process																						IMP
Biological Process	GO:0006783	heme biosynthetic process																						IMP
Biological Process	GO:0006810	transport	ISA	ISA
Biological Process	GO:0006824	cobalt ion transport															IMP				IDA	IDA		IDA ISO		IDA		IGI
Biological Process	GO:0006825	copper ion transport														IMP					IDA	IDA		ISO			IGI
Biological Process	GO:0006826	iron ion transport															IMP			IMP			IMP ISO	IDA IMP			IGI		IMP
Biological Process	GO:0006828	manganese ion transport	IEP	IEP			TAS	TAS		TAS							IMP			ISS	IDA	IDA	IMP	ISO			IMP	IMP
Biological Process	GO:0006829	zinc ion transport																IGI
Biological Process	GO:0006875	cellular metal ion homeostasis			NAS	NAS	NAS	NAS	NAS	NAS
Biological Process	GO:0006876	cellular cadmium ion homeostasis																IGI		IGI			ISO				IGI
Biological Process	GO:0006877	cellular cobalt ion homeostasis																										IGI
Biological Process	GO:0006878	cellular copper ion homeostasis																									IGI
Biological Process	GO:0006879	cellular iron ion homeostasis								IGI					IDA IMP					IMP	TAS	TAS	IMP ISO						IMP
Biological Process	GO:0006909	phagocytosis													IEP					ISS			IMP
Biological Process	GO:0006915	apoptosis																			IDA
Biological Process	GO:0006919	activation of caspase activity																			IDA	IDA		ISO
Biological Process	GO:0006950	response to stress											IMP
Biological Process	GO:0006954	inflammatory response																		ISS			IMP
Biological Process	GO:0007035	vacuolar acidification																		ISS			IMP
Biological Process	GO:0007611	learning or memory																						IMP
Biological Process	GO:0008150	biological process																							ND
Biological Process	GO:0009617	response to bacterium						IEP							IMP					IDA			IMP ISO
Biological Process	GO:0009624	response to nematode								IEP
Biological Process	GO:0010038	response to metal ion									IGI	IGI	IGI	IDA
Biological Process	GO:0010039	response to iron ion								IEP				IDA							IEP NOT IEP	IEP NOT IEP				IEP
Biological Process	GO:0010043	response to zinc ion						IEP
Biological Process	GO:0010288	response to lead ion																								IEP
Biological Process	GO:0010628	positive regulation of gene expression																		ISS			IMP
Biological Process	GO:0010670	positive regulation of oxygen and reactive oxygen species metabolic process						IGI		IGI
Biological Process	GO:0015674	di-, tri-valent inorganic cation transport														IGI
Biological Process	GO:0015675	nickel ion transport																			IDA	IDA		ISO
Biological Process	GO:0015676	vanadium ion transport																			IDA	IDA		ISO
Biological Process	GO:0015677	copper ion import														IMP
Biological Process	GO:0015684	ferrous iron transport															IMP				IDA	IDA		IDA ISO		IMP
Biological Process	GO:0015691	cadmium ion transport					TAS	TAS		TAS							IDA IMP										IGI
Biological Process	GO:0015692	lead ion transport					TAS	TAS		TAS											IDA	IDA		ISO		IDA
Biological Process	GO:0015707	nitrite transport																		ISS			IDA
Biological Process	GO:0015992	proton transport																			IDA	IDA	ISO	IDA ISO
Biological Process	GO:0030001	metal ion transport			ISS NAS	ISS NAS	TAS	TAS	ISS NAS	TAS							IMP
Biological Process	GO:0030026	cellular manganese ion homeostasis																									IMP	IMP		IGI
Biological Process	GO:0032147	activation of protein kinase activity																		ISS			IMP
Biological Process	GO:0032496	response to lipopolysaccharide																		ISS			IDA IMP ISO
Biological Process	GO:0032623	interleukin-2 production																		ISS			IMP
Biological Process	GO:0032632	interleukin-3 production																		ISS			IMP
Biological Process	GO:0032729	positive regulation of interferon-gamma production																		ISS			IMP
Biological Process	GO:0033212	iron assimilation														IDA
Biological Process	GO:0034341	response to interferon-gamma																		ISS			IDA
Biological Process	GO:0034599	cellular response to oxidative stress											IMP				IGI				IDA	IDA		ISO
Biological Process	GO:0034755	iron ion transmembrane transport													IDA IMP							EXP		ISO		IDA
Biological Process	GO:0035162	embryonic hemopoiesis												IMP
Biological Process	GO:0035434	copper ion transmembrane transport																			IDA	IDA		ISO		IDA
Biological Process	GO:0035444	nickel ion transmembrane transport																			IDA	IDA		ISO		IDA
Biological Process	GO:0042060	wound healing																		ISS			IMP
Biological Process	GO:0042116	macrophage activation																		ISS			IDA IMP
Biological Process	GO:0042541	hemoglobin biosynthetic process												IMP
Biological Process	GO:0042742	defense response to bacterium						IMP		IMP										ISS			IMP
Biological Process	GO:0042832	defense response to protozoan																		ISS			IMP
Biological Process	GO:0043091	L-arginine import																		ISS			IDA
Biological Process	GO:0045342	MHC class II biosynthetic process																		ISS			IMP
Biological Process	GO:0045730	respiratory burst																		ISS			IDA
Biological Process	GO:0045944	positive regulation of transcription from RNA polymerase II promoter																		ISS			IMP
Biological Process	GO:0046686	response to cadmium ion																								IEP
Biological Process	GO:0046688	response to copper ion												IDA
Biological Process	GO:0046718	viral entry into host cell														IMP
Biological Process	GO:0048002	antigen processing and presentation of peptide antigen																		ISS			IMP
Biological Process	GO:0048255	mRNA stabilization																		ISS			IMP
Biological Process	GO:0048813	dendrite morphogenesis																						IMP
Biological Process	GO:0048821	erythrocyte development																						IMP
Biological Process	GO:0050766	positive regulation of phagocytosis																		ISS			IMP
Biological Process	GO:0050829	defense response to Gram-negative bacterium																		ISS			IMP
Biological Process	GO:0050916	sensory perception of sweet taste														IMP
Biological Process	GO:0055070	copper ion homeostasis														IMP
Biological Process	GO:0055071	manganese ion homeostasis									IMP	IMP	IMP
Biological Process	GO:0055072	iron ion homeostasis									IMP	IMP	IMP							ISS			IMP
Biological Process	GO:0055076	transition metal ion homeostasis														IMP
Biological Process	GO:0055085	transmembrane transport																		TAS	TAS	TAS
Biological Process	GO:0060586	multicellular organismal iron ion homeostasis														IDA				ISS	IMP	IMP	IMP	IMP ISO
Biological Process	GO:0070482	response to oxygen levels																											IEP
Biological Process	GO:0070574	cadmium ion transmembrane transport																IGI		IGI	IDA	IDA	ISO	ISO		IDA
Biological Process	GO:0070627	ferrous iron import																	TAS		IDA	IDA		IDA IMP ISO
Biological Process	GO:0070838	divalent metal ion transport														IGI
Biological Process	GO:0070839	divalent metal ion export																ISS		ISS			IDA
Biological Process	GO:0071421	manganese ion transmembrane transport																		ISS	IDA	IDA		ISO		IDA				IMP TAS
Biological Process	GO:0071577	zinc ion transmembrane transport																			IDA	IDA		ISO
Cellular Component	GO:0000329	fungal-type vacuole membrane																											IDA
Cellular Component	GO:0005575	cellular component																							ND
Cellular Component	GO:0005634	nucleus																			IDA	IDA		ISO
Cellular Component	GO:0005635	nuclear envelope																IDA	IDA
Cellular Component	GO:0005737	cytoplasm																			IDA	IDA		ISO		IDA
Cellular Component	GO:0005739	mitochondrion																										IDA
Cellular Component	GO:0005764	lysosome																		ISS	IDA	IDA	IDA	ISO
Cellular Component	GO:0005765	lysosomal membrane																			IDA	IDA		ISO		IDA
Cellular Component	GO:0005768	endosome																						IDA
Cellular Component	GO:0005769	early endosome																			IDA	IDA		IDA ISO
Cellular Component	GO:0005770	late endosome																		ISS	IDA	IDA	IDA IMP	ISO
Cellular Component	GO:0005773	vacuole																			IMP	IMP	IMP	ISO
Cellular Component	GO:0005774	vacuolar membrane						IDA		IDA
Cellular Component	GO:0005783	endoplasmic reticulum																												IDA
Cellular Component	GO:0005802	trans-Golgi network													IDA						IDA	IDA		ISO
Cellular Component	GO:0005886	plasma membrane														IDA NAS	IDA	IDA IMP	IDA	IMP	IDA IMP TAS	EXP IDA IMP	ISO	IDA ISO			IDA
Cellular Component	GO:0005887	integral to plasma membrane														ISM NAS	IDA			NAS				IDA
Cellular Component	GO:0005903	brush border																						IDA
Cellular Component	GO:0009279	cell outer membrane																					IDA
Cellular Component	GO:0009986	cell surface																			IDA	IDA	NOT IDA	IDA ISO
Cellular Component	GO:0010008	endosome membrane																					IDA
Cellular Component	GO:0012505	endomembrane system																						IDA
Cellular Component	GO:0012506	vesicle membrane													IDA
Cellular Component	GO:0016020	membrane													IDA	IDA
Cellular Component	GO:0016021	integral to membrane	ISA	ISA													IMP							ISO		IDA	ISM	ISM	ISM
Cellular Component	GO:0016023	cytoplasmic membrane-bounded vesicle																										IDA
Cellular Component	GO:0016324	apical plasma membrane									IDA	IDA	IDA								IDA	IDA		ISO
Cellular Component	GO:0030176	integral to endoplasmic reticulum membrane																												IC
Cellular Component	GO:0030670	phagocytic vesicle membrane																		IDA			IDA IMP ISO
Cellular Component	GO:0031410	cytoplasmic vesicle																			IDA	IDA		ISO
Cellular Component	GO:0031902	late endosome membrane																		TAS	IDA	IDA		ISO		IDA
Cellular Component	GO:0032010	phagolysosome													IDA
Cellular Component	GO:0043229	intracellular organelle										IDA
Cellular Component	GO:0044444	cytoplasmic part														IDA
Cellular Component	GO:0045177	apical part of cell																			IDA	IDA		ISO		IDA
Cellular Component	GO:0045178	basal part of cell																			IDA	IDA		ISO
Cellular Component	GO:0045335	phagocytic vesicle													IDA
Cellular Component	GO:0048471	perinuclear region of cytoplasm																			IDA	IDA		ISO
Cellular Component	GO:0055037	recycling endosome																			IDA	IDA		IDA ISO
Cellular Component	GO:0070821	tertiary granule membrane																		IDA			ISO
Cellular Component	GO:0070826	paraferritin complex																			IDA	IDA		ISO
Molecular Function	GO:0003674	molecular function																							ND
Molecular Function	GO:0005215	transporter activity											ISS
Molecular Function	GO:0005375	copper ion transmembrane transporter activity														IMP					IDA	IDA		ISO		IDA
Molecular Function	GO:0005381	iron ion transmembrane transporter activity												IDA	IDA	IMP					IDA	EXP		IDA ISO		IDA
Molecular Function	GO:0005384	manganese ion transmembrane transporter activity					TAS	TAS		TAS						IMP	IMP			ISS	IDA	IDA	IMP	ISO		IDA				TAS
Molecular Function	GO:0005385	zinc ion transmembrane transporter activity																IGI			IDA NOT IDA	IDA NOT IDA		ISO
Molecular Function	GO:0005506	iron ion binding																						ISO		IDA
Molecular Function	GO:0005507	copper ion binding																						ISO		IDA
Molecular Function	GO:0005515	protein binding																			IPI	IPI
Molecular Function	GO:0008270	zinc ion binding																						ISO		IDA
Molecular Function	GO:0015078	hydrogen ion transmembrane transporter activity															IMP							IDA
Molecular Function	GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity																			IGI						IDA	IDA
Molecular Function	GO:0015085	calcium ion transmembrane transporter activity																			NOT IDA	NOT IDA
Molecular Function	GO:0015086	cadmium ion transmembrane transporter activity															IMP	IGI			IDA	IDA		ISO		IDA
Molecular Function	GO:0015087	cobalt ion transmembrane transporter activity																			IDA	IDA		IDA ISO		IDA
Molecular Function	GO:0015093	ferrous iron transmembrane transporter activity																			IDA	IDA		IDA ISO		IMP
Molecular Function	GO:0015094	lead ion transmembrane transporter activity																			IDA	IDA		ISO		IDA
Molecular Function	GO:0015099	nickel ion transmembrane transporter activity																			IDA	IDA		ISO		IDA
Molecular Function	GO:0015100	vanadium ion transmembrane transporter activity																			IDA	IDA		ISO
Molecular Function	GO:0015103	inorganic anion transmembrane transporter activity			ISS	ISS	ISS	ISS	ISS	ISS
Molecular Function	GO:0015292	uniporter activity															IMP
Molecular Function	GO:0015293	symporter activity														IGI	IDA IMP
Molecular Function	GO:0015295	solute:hydrogen symporter activity																			IDA	IDA		ISO			IDA
Molecular Function	GO:0016151	nickel cation binding																						ISO		IDA
Molecular Function	GO:0022890	inorganic cation transmembrane transporter activity																			IGI	IGI		ISO			IDA	IDA
Molecular Function	GO:0030145	manganese ion binding																						ISO		IDA
Molecular Function	GO:0042803	protein homodimerization activity																		IDA			ISO
Molecular Function	GO:0046870	cadmium ion binding																						ISO		IDA
Molecular Function	GO:0046873	metal ion transmembrane transporter activity			ISS NAS	ISS NAS	TAS	TAS	ISS NAS	TAS																			ISS
Molecular Function	GO:0046915	transition metal ion transmembrane transporter activity									ISS	ISS	ISS					IGI		IGI			ISO
Molecular Function	GO:0050897	cobalt ion binding																						ISO		IDA
Molecular Function	GO:0051139	metal ion:hydrogen antiporter activity																IGI		IGI			ISO
Molecular Function	GO:0070835	chromium ion transmembrane transporter activity																			NOT IDA	NOT IDA
Biological Process	GO:0010042	response to manganese ion	IEP	IEP							IMP	IMP	IMP											ISO		IMP

Notes

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When a fusion to a reporter protein, such as GFP or PhoA, is used to determine the localization of a membrane protein, is it appropriate to use the IDA evidence code? Based on a search of the Gene Ontology website, that seems to be what dictyBASE and SGD have done in the past. Is that still the case? Debby (WB also annotates membrane protein::GFP fusions to CC terms using the IDA evidence code. --Kimberly)

Does functional expression inform subcellular localization? For example, if a transporter is expressed in Xenopus oocytes and experiments demonstrate functional transporter activity, can a Cellular Component annotation be made? If so, with what evidence code? --Kimberly

For just the mammalian A1 genes see Category:SLC11A1

Minutes

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SLC11A1/2 Jamboree Notes

Summary of Action Items (also embedded in context of discussion below)

ACTION ITEM: Debby could send a link to where E. coli group was looking in the documentation regarding IDA vs IMP for subcellular localization of fusion proteins

ACTION ITEM: (from ruth) next jamboree, decide on proteins, try to encourage ontology experts for relevant branches of the ontology to participate

ACTION ITEM: add equivalent metal ion terms to the ontology for different metal ions

ACTION ITEM: there's a link to the binding term documentation on the talk page - please give feedback to work out a range of opinions before the consortium meeting

ACTION ITEM create a wiki page where people can start suggesting/annotating genes for future jamborees to encourage broader participation

Items from talk page:

Jim and Brenley - can you use IDA or IMP if you are measuring the localization of a GFP-fusion protein?

Emily - GOA uses IDA if localization is intended to be a measure of the wild-type protein Don't really use IMP for localization annotations. IDA or not at all.

Pascal - Only time to use IMP would be for comparing WT vs mutant protein.

Debby - seems reasonable What is in the evidence code documentation? SGD and dicty both use IDA.

Could improve the documentation.

ACTION ITEM: Debby could send a link to where E. coli group was looking in the documentation.

Related component question:

Does a functional assay inform localization?

GOA would annotate to a component term using IDA.

MGI, WormBase, coli would use IC in these cases, as there is no direct localization data.

Isn't the functional assay enough?

Jim: isn't this analogous to a TF localizing to the nucleus? This is the example on the GO evidence code documentation page.

How do these two situations differ? What actually happens in transfection experiments when a reporter and a TF are transfected together?

Could we leave this issue up to the individual curator?

Wasn't the point of IC to illustrate that there was no direct evidence? Isn't IC a safer annotation?

Two experiments: measure transporter activity AND immunolocalization test to show membrane location Would this be better?

Is expression in an oocyte reflective of normal localization? This is a general concern for expressing a protein outside of its normal environment.

Pascal: problem with IC -- there are two kinds: those based on ISS, those based on a direct assay a cc annotation in this case would be more like one based on a direct assay

Ruth: if these people have actually done an immunofluorescence assay, would we be happy with an IDA if you're showing its functional, it's like doing an immunofluoresence assay

Li: we agree that we don't transfer IC from ISS? if there is experimental evidence, we can use IC

the documentation, however, allows IC from ISS or even IEA

Susan: try to find experimental evidence first would favor annotation to species being annotated, though

Annotating to transport process terms from transporter activity assays

Emily - found a number of papers measured the capacity of this gene product to transport a number of different cations transported, but only a few of these have evidence for a proper physiological basis iron, manganese, possibly lead or copper, but authors also cite experiments for cadmium, cobalt, nickel, etc. across membranes

some of the cations don't seem to have any obvious usefulness in the human body we were quite unsure of how to annoate these experiments. came across a paper where the research community seemed unsure of which transport functions are relevant could there be a role in detox of metal ions?

it's interesting that it has this activity, it'd be useful to see the full range of activities

GOA has annotated individually for each of the different transport activities and also included some NOT annotations

the question: what biological process annotations? for only a few annotations is there physiological relevance known?

could annotate to ion transport, but do we want to provide transport processes for each of the ions transported e.g. cobalt ion transport. link MF and BP annotations? how far to go? investigators aren't sure themselves, assay all sorts of cations for this protein this is a normal wild-type protein just being assayed for different types of transport

Pascal: in terms of tranpsort, the mf and bp terms are essentially synonymous

Tanya: make the process annotations as well as the MF annotations

Emily: normally it would never come into contact with these ions, e.g. vanadium

vanadium is used in some drugs

E: investigators acknowledge a grey area for what is physiologically relevant

Tanya: down the road, someone might be experimenting with these ions and looking for transport(er) terms

P: the function and the process are essentially synonymous is there a situation where you would not make the transport annotation for the transporter activity?

No.

Debby: another example--one of the recent ref genome targets there were e. coli enzymes that were shown to hydrolyze a whole bunch of sugar substrates, all have a broad range of overlapping activities, but it's not clear what biological process those activities are associated with. debby felt comfortable annotating showing the activity, but was hesitant to say it was involved in the substrate metabolism without additional evidence.

Jodi: typically would not make an annotation to process, for in vitro assay, would just leave the function annotation

debby: should we annotate to the biological transport process?

pascal: also depends upon the genomic context - if you have a single enzyme, it's probably the one involved in the process

susan: annotate according to the intent of the authors - annotate to metal ion transport, but not each individual transport term.

ruth: affinities could inform the annotations - what are relevant levels of solutes? agree with susan, if the authors were quite hesitant, unless curators feel confident authors are dealing with physiological levels of ions, then make the annotation.

debby: there's a difference between going with what the authors intend vs going past what the authors intend

tanya: but then why do they present the data? we're annotating to the experiments.

pascal: authors don't really know the significance

emily: it does seem the affinity for transport doesn't necessarily correlate with in vivo activity

pascal: an annotation to lead transporter activity, why not to lead transport?

ruth: several papers and reviews have been published, numerous groups are not willing to say that these proteins are involved in a given metal ion transport process

tanya: the structure of the ontology is such that metal ion transport will be found if annotations are made to the more specific child term

what ions are physiologically relevant?

why would the terms be in the ontology if they weren't biologically informative?

pascal: humans have evolved ways to deal with all kinds of toxic chemicals

debby: reading the introduction of the paper that emily put the pubmed id up for--this protein is a widely expressed ferrous iron transport that plays a vital role in iron homeostasis, general agreement for role in iron transport biochemically common to check other ions to characterize the transporter, but how specific are the transporter activites? would feel very confident annotating to metal ion transport and maybe based on other papers annotate to more specific biological process terms. wouldn't feel comfortable annotating to more specific terms from this paper, unless there was some other evidence that is was involved in that biological process. mf annotations would help people get to these gps.

discussion of transport terms

ruth: think about the intent of the authors. in this case, the authors don't intend to prove that cadmium is transported by this protein. because there are so many different metal ion transporters, you can't be sure which ones actually tranport in vivo

tanya: the potential is what can be annotated

ruth: the authors do not intend to show that this is the enzyme that actually does this process. could do this experiment with a variety of different transporters, but that isn't the experiment they did.

pascal: how would you be convinced, in human, to annotate to iron transport?

ruth: if there was a mutation in humans that affected iron levels, that would be very good evidence.

pascal: but these are very large gene families

ruth: but the authors don't intend to prove that this particular transporter is involved in this process

Homeostasis term annotations

emily: when to annotate to homeostasis terms? this protein transports ions and knock-outs are associated with anemia? do people co-annotate to iron homeostasis? homeostasis is the regulation of the process of ion transport? can't get homeostasis if the transporter is knocked out how much information is needed for an IMP annotation to iron homeostasis?

would anyone have a problem with iron homeostasis?

No, sounds reasonable.

should iron transport be related to iron homeostasis? should transport be a part_of homeostasis?

would you have a term, vanadium homeostasis?

how do people feel about a formal part_of link between transport and homeostasis?

if you're moving ion levels around, aren't you also affecting the homeostatic process? is this a leap too far? maybe just put a comment in for the transport term

would probably want to annotate to homeostasis if you were convinced that ion actually had a role in your organism maybe that's a reason for putting this into the comments for the term

petra: would now annotate to homeostasis terms for the dicty protein

jim: iron homeostasis seems to be a very central role for the transporters would you make a homeostasis annotation for a calcium transporter?

ruth: return of levels of calcium to resting state could be annotated to homeostasis

pascal: was anyone involved in the reorganization of the transport branches of the ontologies?

tanya: there was a transport group...who was in it?

pascal: have transport annotation guidelines? some very basic things we're talking about, but we don't all seem to be annotating the same way

ACTION ITEM: (from ruth) next jamboree, decide on proteins, try to encourage recent ontology experts to participate

Ontology development for metal ion terms

emily: creating different annotations for different metal ions because there's a lack of terms to describe different metal ions equivalent terms for iron and manganese don't exist

ACTION ITEM: add equivalent metal ion terms to the ontology for different metal ions

Binding term documentation
ruth: binding terms

had a binding term annotation conference call ruth has written out the minutes and proposed guidelines please take a look

from the meeting, we were not going to do any ICs for binding?

the concepts discussed in the binding meeting--if a protein has iron transport activity, you don't have to annotate to iron binding if there's a direct experiment to test for iron binding, then add the annotation otherwise, just annotate to the transport activity

debby: thought the conclusion was that you didn't need to do it, but that it was okay to do it

ruth: it'd be really great to finish off this documentation. if this is still not clear, then the binding discussion group needs to sort this out.

it'd be good to resolve this and get the proposal agreed upon at the September consortium meeting.

ACTION ITEM: there's a link to the binding term documentation on the talk page - please give feedback to work out a range of opinions before the consortium meeting

Suggestions for jamboree genes to encourage broader participation

emily: a really good idea from Li regarding selection of targets

have a table of a number of potential targets, each group could indicate the number of papers to help get maximal participation in the calls

mgi/goa are often overwhelmed by the number of papers, other groups have very little literature

ACTION ITEM:pascal: start making the page now and people can start suggesting/annotating the genes

References

See Help:References for how to manage references in GONUTS.

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D

E

ECOLI:mntH

F

FB:Mvl

H

H cont.

HUMAN:Q8IUD7

M

R

S

T

TAIR:AT1G15960.1

T cont.

W

Z

ZFIN:slc11a2

Category:RefGenome Electronic Jamboree 2009-07 SLC11A1/2

Contents

Orthoset

Participants

Annotations

Biological Process graph

Cellular Component graph

Molecular Function graph

Genes needing annotation

Notes

Minutes

References

Pages in category "RefGenome Electronic Jamboree 2009-07 SLC11A1/2"

C

D

E

F

H

H cont.

M

R

S

T

T cont.

W

Z

r

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