hupo-psi / psi-mi-cv Goto Github PK

Required for PSI-MI 2.5 schema. Current contents

N-terminus
Ragged N-terminus

C-terminus

Undetermined

Certain

Less than

More than

Reported by: orchard

A number of groups in the BioPAX workgroup have
expressed interest in an ‘indirect interaction’ term to
capture the case when a curator has inferred that a
published interaction has not been proven to involve
only its interactors. Users could choose to trust the
curator’s opinion of this flag or could decide on their
own based on the experimental evidence whether they
think the interaction has been proven to be direct.
This can be a matter of opinion, as certain cases,
biochemists may disagree about the proof of directness
or to put it another way, might agree on 100% direct
proof, but be satisfied by different likelihoods of
being direct e.g. 80% or 90%

Reported by: gbader

In response to Gary’s e-mail

Reported by: orchard

for genetic interaction proposal for biological role
suppressor, supressed
for fret idea for experimental role
donor aceptor (could support electron transfert or
fluorescence resonance)

Reported by: luisa_montecchi

in CV database citation to cover papers pre published
without PUBMED ID

Reported by: luisa_montecchi

Sumoylated lysine is a PTM term, but no corresponding
sumoylation interaction type term exists. In general,
should the interaction type tree mirror the PTM tree
completely?

Reported by: gbader

The sequence ontology (SO) includes a number of terms
similar to terms currently under interactor
type->biopolymer

Should we just use SO here instead?

http://genomebiology.com/2005/6/5/R44

Reported by: gbader

3-Hybrid
-————
A technic to show a ternary complex :
- protein A fused to DB (DNA Binding domain)
- protein B
- protein C fused to AD (Activation Domain)
If there is reporter transcription, you will know that (with
the correct controls) :
protein A binds proteins B which binds protein C:
- A binds B
- B binds C
- interaction between A and C is indirect (part of the
same complex)
How to curate this ?
all as neutral components but we loose the information
of directionality
B as the bait, A and C as the preys but we loose the
information that it B can bind A and C at the same time.
The detection technics added is ’ two hybrid’ for the
moment but through the rule the bait should be the one
with the DB domain (A), not really the best here.
A new term is needed. The caution fro the name is that
rna tri hyrbid has already triple hybrid system as a
synonym.

PMID : 16080001

It differs from:

term: tri hybrid
id: MI:0437
definition: cDNA encoding the bait, the prey and a third
protein component is transfected into a recombinant
yeast strain for library transformation. \nOBSOLETE
this is a two hybrid variation remap to “two hybrid”
(MI:0018) , or to “rna tri hybrid” (MI:0438)
definition_reference: PMID:12761205
definition_reference: PMID:12935900
definition_reference: PMID:12052864

term: dhfr reconstruction: dihydrofolate reductase
reconstruction
id: MI:0111
definition: The gene for DHFR is rationally dissected into
two fragments called F[1,2] and F³. Two proteins or
protein domains that are thought to bind to each other
can then be fused to either of the two DHFR fragments.
Reconstitution of enzyme activity can be monitored in
vivo by cell survival in DHFR-negative cells grown in the
absence of nucleotides. A fluorescence assay can also
be carried out taking advantage of fMTX (the third
element of the so called triple hybrid essay) binding to
reconstituted DHFR. The basis of this assay is that
complementary fragments of DHFR, when expressed
and reassembled in cells, will bind with high affinity (Kd
5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in
cells by this complex, whereas the unbound fMTX is
actively and rapidly transported out of the cells. Survival
depends only on the number of molecules of DHFR
reassembled.
definition_reference: PMID:10318894

term: rna tri hybrid
id: MI:0438
definition: In vivo reconstruction of specific RNA-proteins
interactions. The DNA binding and transcription activator
domains of GAL4 are brought together via the
interaction of recombinant RNA. The first hybrid protein
contains the DNA binding domain of GAL4 fused to
RevM10 (a mutated RNA binding protein of HIV-1 that
binds specifically to the Rev responsive element RRE of
the env gene). A recombinant RNA contains the RRE
sequence and a target RNA sequence X. The second
hybrid protein contains the activation domain of GAL4
fused to protein Y tested for its ability to bind the target
RNA X. If this interaction occurs the three hybrid
reconstructs GAL4 and the transcription of a reporter
gene is activated.
definition_reference: PMID:8972875
definition_reference: PMID:12162957

Karine

Reported by: krobbe4

MI :0343

Reported by: luisa_montecchi

We currently have in the CVs a small list of
experimental condition with the following terms
(created in Nice PSI meeting 2004):
in vitro
-in silico
-in vivo
--in situ

This CV has no correponding element is the PSI XML
structure, basically because this information can
reported in the EXPERIMENT , under HOST ORGANISM
using as Taxid == 0 for in vitro and the appropriate
Taxid when the interaction occur in a given organism.

Should be decided whether this CV is deleted (as nobody
seam to have notice the missing element within PSI XML)
or instead a corresponding element is created.

Reported by: luisa_montecchi

in vitro translated protein

Reported by: luisa_montecchi

Term: reconstituion assay
Definition: A in vitro simulation of a in vivo process
by putting together
purified or partially purified components of the system.
PMID: Have your pick

1: Gummadi SN, Hrafnsdottir S, Walent J, Watkins
WE, Menon AK. Related
Articles, Links
No abstract Reconstitution and assay of biogenic
membrane-derived
phospholipid flippase activity in proteoliposomes.
Methods Mol Biol. 2003;228:271-9. No abstract available.
PMID: 12824560 [PubMed – indexed for MEDLINE]
2: Xu Z, Kandror KV. Related Articles, Links
Free Full Text Translocation of small preformed
vesicles is responsible
for the insulin activation of glucose transport in
adipose cells. Evidence
from the in vitro reconstitution assay.
J Biol Chem. 2002 Dec 13;277(50):47972-5. Epub 2002 Oct 21.
PMID: 12393900 [PubMed – indexed for MEDLINE]
3: Boiret N, Kanold J, Fouassier M, Bons JM, Halle
P, Rapatel C, Berger
J, Pireyre P, Blanzat V, Travade P, Bonhomme J, Demeocq
F, Berger
MG. Related Articles, Links
Abstract CFU-Mk content of immunoselected CD34+
peripheral blood
progenitor cells, evaluated with an adapted serum-free
methylcellulose
assay, is predictive of platelet lineage reconstitution
in children with
solid tumors.
J Hematother Stem Cell Res. 2000 Aug;9(4):525-34.
PMID: 10982252 [PubMed – indexed for MEDLINE]
4: Inoue G, Cheatham B, Kahn CR. Related
Articles, Links
Free in PMC Development of an in vitro
reconstitution assay for
glucose transporter 4 translocation.
Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14919-24.
PMID: 10611313 [PubMed – indexed for MEDLINE]
5: Vida T, Gerhardt B. Related Articles, Links
Free Full Text A cell-free assay allows reconstitution of
Vps33p-dependent transport to the yeast vacuole/lysosome.
J Cell Biol. 1999 Jul 12;146(1):85-98.
PMID: 10402462 [PubMed – indexed for MEDLINE]
6: Chanda B, Mathew MK. Related Articles, Links
Abstract Functional reconstitution of
bacterially expressed human
potassium channels in proteoliposomes: membrane
potential measurements
with JC-1 to assay ion channel activity.
Biochim Biophys Acta. 1999 Jan 12;1416(1-2):92-100.
PMID: 9889332 [PubMed – indexed for MEDLINE]
7: Bremers AJ, van der Burg SH, Kuppen PJ, Kast
WM, van de Velde CJ,
Melief CJ. Related Articles, Links
Abstract The use of Epstein-Barr
virus-transformed B lymphocyte
cell lines in a peptide-reconstitution assay:
identification of
CEA-related HLA-A*0301-restricted potential cytotoxic
T-lymphocyte
epitopes.
J Immunother Emphasis Tumor Immunol. 1995 Aug;18(2):77-85.
PMID: 8574469 [PubMed – indexed for MEDLINE]
8: Groesch ME, Rossi G, Ferro-Novick S. Related
Articles, Links
No abstract Reconstitution of endoplasmic reticulum
to Golgi transport
in yeast: in vitro assay to characterize secretory
mutants and functional
transport vesicles.

Reported by: luisa_montecchi

Add detail of tags to Experimental Form to describe
type of tag attached to protein (in IntAct this will
add detail to our protein feature descriptions)

New parent terms with parent
Experimental form/Tagged-protein

1. FLAG-tagged
2. HA-tagged
3. GST-tagged
4. Myc-tagged
5. His-tagged
6. TAP-tagged
7. V5-tagged
8. GST-tagged
9. T7-tagged

Reported by: orchard

Required for PSI-MI 2.5 schema. Current contents

Method

Identity

Primary-reference

Secondary-reference

See-also

Compenent

Process

Subcellular location

Reported by: orchard

‘endag’ the graph so that feature detection method have
inference and prediction as children

Reported by: luisa_montecchi

terms being used in Intact as ‘annotation topic’
for each term query with the EBI-AC at:
http://www.ebi.ac.uk/intact/search/do/search
Other PSI partners ‘annotation topic’ are welcome to
try to map corresponding topic and formalize them in
the appropriate PSI CV.

EBI-AC NAME DEFINITION ATTACHED TO
EBI-15 comment Comment for public view “Interaction,
Experiment, Cv, Protein, BioSource”
EBI-16 function Biological function of the protein or
the interaction “Protein, Interaction”
EBI-18 url URL/Web address “Experiment, Interaction,
Cv, BioSource”
EBI-22 search-url Search engine URL. Cv Database
EBI-24 example Example Cv
EBI-296010 disease The interaction has a disease
association. Interaction
EBI-296169 caution Warning about errors/ grounds for
confusion. “Interaction, Experiment, Cv, Protein”
EBI-296170 pathway Refers to the metabolic pathway that
the interaction/complex is involved in. Interaction
EBI-300002 search-url-ascii Search URL to retrieve an
external entry in ASCII format Cv Database
EBI-300444 author-confidence Confidence classification
assigned by the author of the publication Interaction
EBI-300446 confidence-mapping Description of confidence
mappings in the experiment Experiment
EBI-447469 inhibition Inhibitor of an interaction.
Interaction
EBI-448599 stimulation Stimulator of an interaction.
Interaction
EBI-448603 agonist Activator of an interactor.
Interaction
EBI-448606 antagonist Inactivator of an interactor.
Interaction
EBI-458504 exp-modification Modifications of an the
standard experimental method described in the CV
Experiment
EBI-464829 kinetics Data related to kinetics of
enzymes. Interaction
EBI-516793 id-validation-regexp Regular Expression used
to check the validity of cross references’
identifier. Cv Database
EBI-520726 copyright Description of the copyright under
which the data is distributed. Experiment
EBI-533435 complex-properties Information on the
complex being annotated. Interaction
EBI-540770 3d-structure Comments on the 3D structure
Interaction
EBI-540772 3d-r-factors Free R-Factor and working
R-Factor for the quality of the crystallographic
model Interaction
EBI-540774 3d-resolution Resolution of the 3D
structure Interaction
EBI-597783 data-processing Information about how the
data was processed- mainly for large scale data.
Experiment
EBI-602911 contact-email E-mail address to contact the
author/organisation which has produced the data
Experiment
EBI-602931 contact-comment Free text notes on how to
contact the author organisation which has produced
the data. Experiment
EBI-633457 author-list List of authors associated to
a publication Experiment
EBI-81510 isoform-comment Protein isoform’s comment for
public view “Interaction, Protein”
EBI-872 prerequisite-ptm PTM required for an
interaction to occur. Interaction
EBI-877 resulting-ptm PTM occurs subsequent to
interaction occuring Interaction

Reported by: luisa_montecchi

Required for PSI-MI 2.5 schema. Current contents

gene-name,
synonym-name,
orf-name,
locus-name

Reported by: orchard

move all enzymatic reaction under direct interaction

Reported by: luisa_montecchi

Dyes (for any kind of molecule), rare isotope (13C,
15N, 2H) that are not radioactive can be used as
labels as well.

Reported by: luisa_montecchi

To accompany Kinetics CV – these are purely as required
by the kinetics CV to date, additional terms may need
additional units.

Sandra

Units
- Concentration
\ Molar syn M
\ millimolar syn mM
\ micromolar syn uM
\ nanomolar syn nM
\ picomolar syn pM

\- Time
\ seconds syn secs

Reported by: orchard

This is mainly a BioPAX/pathway database compatility issue.

It is difficult to figure out if a binding event
creates a complex in the current interaction type CV.
“direct interaction” looks like it might be the correct
term to signify this, but it seems to be too general.
Maybe a term called “complex assembly” (to match the
BioPAX complexAssembly class) could be added as a child
of direct interaction (or mayb direct interaction means
complex assembly, in which case ‘complex assembly’
could be added as a synonym.

This is not the case for enzymatic reactions and
BioPAX, since there is a clear interaction type for this.

Thanks,
Gary

Reported by: gbader

The CytoTrap method is used for finding unique
protein-protein interactions in the cytoplasm. Thu the
proteins are expressed in the cytoplasm where, they may
undergo posttranslational modifications. The bias in
two hybrid of the transcriptional activators and
inhibitors is also lost. Toxic proteins may also be
studied, as the expression of the bait and target
proteins is inducible. We have Reverse ras recruitment
one of the technique using cytotrap in the CV can we
have a parent term cyto trap to cover other
complimentation approaches using imilar systems.

Reported by: jyotikhadake

The definition of a hotspot is a residue of a protein
whose identity modifies significantly interaction
properties. But hotspot are indeed used for residues or
group of residues which when mutated
(substitution/deletion) decrease drastically the
interaction.

For the moment the residues which when mutated can
increase the interaction cannot be recorded.
There can be different cases for increasing of interaction:

case 1)
The residues or fragment is inhibitory for the interaction

case 2)
The residue is not by itself inhibitory but having another
amino-acid there can tighten the interaction. For this
case, it could be misleading to called them ‘coldspot’
or ‘negative’.
The amino acid is changed for example into acidic
amino acid and may mimics a phosphorylation which
increase phosphorylation.
The amino acid is changed into a basic amino acid and
the residue was in the middle of a basic patch so it may
binds even more efficiently to an acidic patch…

NB: it is possible that the same residue when mutated
into an amino-acid will decrease the interaction and
mutated into another one will increase the interaction.

How this mutation effect should be recorded and called
(shortlabel/fullname)?
Should they be children of hostpot?

@is_a@feature detection
@is_a@hotspot
is_a negative effect of the mutation (more
common one)
is_a postive effect of the mutation

or at the same level as hotspot?

@is_a@feature detection
@is_a@hotspot (negative effect of the mutation)
@is_a@postive effect of the mutation

Cheers,
karine (IntAct) and Andrew (MINT)

Reported by: krobbe4

New parent term to “Gel Filtration” and “Affinity
Chromatography” since papers with very short methods
sometimes do not specify details, and some groups use a
combination of methods to purify complexes.

Sandra

Reported by: orchard

Embryonic kinetics CV for your approval/comment.

Kinetics
- Enzyme kinetics
\ IC50
\ Ki
\ Km
\ Kcat

\- Binding kinetics
\ Kd
\ EC50

EC50 � Reaction dependent. The molar concentration of
an agonist, which produces 50% of the maximum possible
response for that agonist under the stated conditions.
Unit M.

IC50 � Reaction dependent. The molar concentration of
an agonist, which produces 50% of the maximum possible
inhibitory response for that agonist under the stated
conditions. Unit M.

Ki � Reaction independent. Equilibrium constant for
inhibitor binding. Unit M

Km � the concentration of substrate at which the
reaction rate is equal to half the maximal rate (i.e.
Km={s} when V0=˝Vmax). This definition is not true for
allosteric enzymes. Unit M
Synonym: Michaelis-Menten constant

Kcat � the number of substrate molecules converted to
product in a given unit of time on a single enzyme
molecule when the enzyme is saturated with substrate.
Unit. Per second
Synonym: Turnover number

Kd – The equilibrium dissociation constant for a
receptor/ligand, or protein A dissociating from protein
B. Unit M.

Reported by: orchard

Required for PSI-MI 2.5 schema. Current contents

Transfection (syn Transformation)

Genomic Tagging/Insertion

Electroporation

Micro-injection

Infection

Reported by: orchard

To be added to “Interaction Detection Method” at same
level as “Experimental” and “Predicted”

Synonyms “Curated” “Modelled”

Definition – Ineraction inferred by a curator or author
on the basis of experimental evidence. This may be by
combining experimental evidencefrom several sources in
the same species or idenifying orthologues in closely
related species.

Reported by: orchard

Should cleavage (MI:0194) be renamed to ‘protein
cleavage’? If it is meant to be general cleavage
(breaking of any covalent bond) then lipid cleavage
should definitely be a child of cleavage.

Reported by: gbader

Similarly method to the exciting interaction detection
method MI:0404 ‘comigration in non denaturing gel
electrophoresis’. As the usage of 2d gels allows to
explore bigger complexes and involves different
technologies, it may worth creating a new term as
children of the above mentioned MI:0404 .

See for application instance of this methods PMID 14730074
The composition and dynamics of membrane protein
complexes were studied in the cyanobacterium
Synechocystis sp. PCC 6803 by two-dimensional blue
native/SDS-PAGE followed by matrix-assisted
laser-desorption ionization time of flight mass
spectrometry. Approximately 20 distinct membrane
protein complexes could be resolved from
photoautotrophically grown wild-type cells. Besides the
protein complexes involved in linear photosynthetic
electron flow and ATP synthesis (photosystem [PS] I,
PSII, cytochrome b6f, and ATP synthase), four distinct
complexes containing type I NADH dehydrogenase
(NDH-1) subunits were identified, as well as several
novel, still uncharacterized protein complexes.

Reported by: luisa_montecchi

Add a common parent term to radio and rare isotope
labelling

Reported by: luisa_montecchi

definition_reference: RESID:AA0055 , AA0056
definition_reference: RESID:AA0078 , AA0059

In the rest of the entries separate ids are split onto separate lines.

-Alan

Reported by: alanr

Method:
enzymatic activity

ligand-cell interaction using alkaline phosphatase
activity:

Cells express the protein of interest, a ligand, as a
protein fusion with alkaline phosphatase. The
supernatant containing this ligand is then added on
other cells expressing the corresponding receptor.
These cells are then washed to remove unbound ligands.
The measure of alkaline phosphatase activity in the
lysate permits to make quantitative studies of ligand
binding to the cells through the receptor.
(Bruckner, 2000) (Sasamura, 2003)

interaction detection :
ligand-cell interaction using alkaline phosphatase activity
participant detection:
predetermined

Proposition :
% enzymatic activity
% enzymatic activity of the protein
% enzymatic activity of the fused protein
% ligand-cell interaction using alkaline
phosphatase activity

The definition of ELISA does not fit because it does
not involved antibodies, blocking agent, and solid phase.

enzyme-linked immuno: enzyme-linked immunosorbent assay

Following non-covalent binding of a purified primary
ligand to a solid phase, a blocking reagent is added to
prevent any non-specific binding. A specific antigen is
then allowed to bind to the primary ligand. Unbound
antigen is removed by washing and a secondary antibody
conjugated to an enzyme (e.g. horseradish peroxidase)
is added. Following a washing step to remove unbound
secondary ligand, the extent to which a chromogenic
substrate (e.g. 3,3’, 5,5’ tetramethyl benzidine
chromogen [TMB]) is converted to a soluble colored
product by the conjugated enzyme in a given time is
determined by spectrophotometry using a standard
microplate absorbance reader. A similar type of
approach can be utilized to detect enzymatic
activities. The substrate, attached to a solid phase is
incubated in the presence of the enzyme and the
enzymatic modification is monitored by an antibody that
is specific for the modified substrate (for instance a
phosphorylated protein).

Reported by: krobbe4

Proposition for two new techniques for detecting
interactions between transmembrane receptors based on
functionnal complementation.
(TOXCAT is only for TM homodimerization)

I would put them as a child of ‘complementation’ rather
than ‘two-hybrid’ because they do not use
complementation between an activation and a DNA binding
domain.

1) GALLEX

Reference:
Schneider D, Engelman DM.
GALLEX, a measurement of heterologous association of
transmembrane helices in a biological membrane.
J Biol Chem. 2003 Jan 31;278(5):3105-11. Epub 2002 Nov 21.
PMID: 12446730

This system permits to follow heterodimerization of
membrane proteins in the Escherichia Coli inner
membrane. This technique can also be used to test
homodimerization and to find homodimerization hotspots.

The method is based on the repression of a reporter
gene activity by two LexA DNA binding domains with
different binding specificities.LexA is a transcription
factor with a N-terminal DNA binding/Activation domain
(DBAct) and a C-terminal dimerization domain.LexA
dimerization is required to repress transcription
efficiently. The discovery of LexA DNA binding domain
that bind to different DNA sequence enabled
the development of this system.

The two fusions proteins are LexA DBAct1-TM1-MBP and
LexA DBAct2-TM2-MBP where TM1 and TM2 are two
transmembrane domains of interest, LexA DBAct1 and LexA
DBACt2 are two DNA binding/activating domain targeting
two different sequences and MBP is the maltose binding
protein. The LexA DNA binding domain is located in the
E. Coli cytoplasm, the transmembrane protein in the
inner membrane and the MBP protein in the periplasm.

Interactions of the two TM domains leads to the
formation of LexA heterodimers, which can bind to the
operator region. The binding of the LexA dimer results
in repression of a reporter gene like LacZ
(beta-galactosidase activity).

2) TOXCAT

Reference:
Russ WP, Engelman DM.
TOXCAT: a measure of transmembrane helix association in
a biological membrane.
Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):863-8.
PMID: 9927659

The system TOXCAT permits the study of transmembrane
helix-helix oligomerization in a natural membrane
environment, the Escherichia Coli inner membrane. The
assay can be used to find dimerization hotspots in
known dimerization TM. It can also be used to select
oligomeric TM in a library of randomized sequences.

This assay uses a chimeric construct ToxR-TM-MBP
composed of the N-terminal DNA binding/transcriptional
activation domain of ToxR (a dimerization dependant
transcription factor) fused to a transmembrane domain
of interest™ and a monomeric periplasmic anchor
(the maltose binding protein).

Association of the two TM results in the ToxR-mediated
activation of a reporter gene like CAT
(chloroamphenicol acetyltransferase activity). The
level of CAT expression indicates the strength of TM
association. CAT expression can then be tested and
quantify by measuring CAM resistance with disk
diffusion assay or CAT activity assays on cell-free
extracts.

Karine

Reported by: krobbe4

Required for PSI-MI 2.5 schema. Current contents

Small molecule

Protein
Peptide

Nucleic acid
DNA

Reported by: orchard

‘proximity calculation’ child of both prediction from
structure and prediction from experimental information.
describing xray atom distance measure among protein
within a complex that lead to interacting domain prediction

Reported by: luisa_montecchi

shortlabel: afcs two-hybrid
fullname: AfCS Yeast 2-Hybrid Interaction Data
definition : Alliance for Cellular Signaling (AfCS Nature)
Yeast 2-Hybrid Interaction Data. Information and data
are freely available to all.
url-search : http://www.signaling
gateway.org/data/Y2H/cgi-bin/y2h.cgi
id: pronet_id of the bait

Karine

Reported by: krobbe4

Binding sites and Hotspots.

It appears there are several ways of using the new
controlled vocabularies of the features. All ways can
be justified but maybe we
should discuss to have a common way to use them.

For Hotspot:

The feature for hotspot is now called ‘mutation
decreasing’ (so mutation decreasing’ could also be
introduced). Hotspots used to be for very short mutations:
- mostly substitions of aminoacid
- deletion of aminoacid
Now, ‘required to bind’ is sometimes used for the
hotspot when the mutation abolish completly the
interaction which has not mutation as parent anymore.
If ‘required to bind’ used, the shortlabel should it be
like a mutation (ie lys289ala) ?
Should there be a threshold amino acid number to use
mutation CVs rather than binding site CVs ?

For Binding site:

Depending on the experiment it can be annotated to :
- sufficient to bind -> deletion analysis showing a
fragment which can still bind
- required to bind -> identify a region which when
deleted prevents interaction but in most of the time,
it may not be sufficient to bind. (usually smaller than
fragments shown to be sufficient to bind)
These two piece of information can be complementary.
Question: Should they be both enter if possible?

Cheers,
Karine

Reported by: krobbe4

New tag : MBP

shortlabel: mbp
full name: MBP-fusion protein
definition : The cloned gene is inserted upstream or
downstream of the malE gene which encodes maltose-
binding protein (MBP). The MBP-fusion protein can be
purifed by affinity chromatography using an amylose
resin.

Karine

Reported by: krobbe4

Required for PSI-MI Level 2.5 schema. Current contents

Endogenous

Over-expressed

Under-expressed

Reported by: orchard

having the follonging high level terms
feature type :
- biological featur
- experimental form

Reported by: luisa_montecchi

In the experimental form CV, how can we distinguish
between N and C terminal tags on proteins. It seems
that the CV terms do not specify. Do we want to
specify this?

Reported by: gbader

add ‘gene’ as an abstract object at top level for
genetic interaction

Reported by: luisa_montecchi

In oder to distinguish the interactor that have a
sequence (nucleic acid and protein) from those who do
not (small molecules, complexes) we propose to add the
term “polymer” in the PSI interactor type.

The new term would be a high level term parent of
protein, nucleic acids the CV would have the following
three:
@is_a@interactor type ; MI:0313
@is_a@complex ; MI:0314
@is_a@protein complex ; MI:0315
@is_a@protein dna complex ; MI:0233
is_a ribonucleoprotein complex ; MI:0316
@is_a@interaction ; MI:0317
@is_a@small molecule ; MI:0328
@is_a@unknown participant ; MI:0329
-new term polymer as parent of :
@is_a@nucleic acid ; MI:0318
@is_a@dna: deoxyribonucleic acid ; MI:0319 ;
@is_a@rna: ribonucleic acid ; MI:0320 ;
@is_a@crna: catalytic rna ; MI:0321
@is_a@grna: guide rna ; MI:0322
@is_a@hnrna: heterogeneous nuclear ribonucleic ;
MI:0323
@is_a@mrna: messenger ribonucleic acid ; MI:0324 ;
@is_a@trna: transfer ribonucleic acid ; MI:0325 ;
@is_a@protein ; MI:0326
@is_a@peptide ; MI:0327

Reported by: luisa_montecchi

New tag : MBP

shortlabel: mbp
full name: MBP-fusion protein
definition : The cloned gene is inserted upstream or
downstream of the malE gene which encodes maltose-
binding protein (MBP). The MBP-fusion protein can be
purifed by affinity chromatography using an amylose
resin.

Karine

Reported by: krobbe4

Library screening and directed two hybrid screening as
children of two hybrid in interaction detection method
CV. Library screening is very common and so also is
directed two hybrid screening. This will also help
check associated participant detection methods.

Reported by: jyotikhadake

Need for this CV agreed by IMEx in Rome, will be part
of PSI 2.5 schema. Current contents

Naturally occurring

Engineered

Reported by: orchard

1 Hybrid
-——
Interaction involving an Activator, can be done in
mammals cells
Protein A fused to DB
Protein B (not fused already have a AD)
If there is reporter transcription, you will know that (with
the good controls) :
protein A binds B
The detection technics added is ‘two hybrid’ for the
moment , but the protein B is not fused to an AD here.
It is a complementation but between a tag on the bait
and the prey ( in 2 hybrid: complementation between
the tag of the bait and the tag of the prey)

The one in the CV: bait = DNA promoter, prey = DBD
protein (with also an activation domain)
-> DNA/protein interaction

The one to be added: bait= DBD protein, prey = activator
-> DBD protein/activator protein interaction.
Here DBD and activator are encoded by different cDNA

It is a bit different so a new term may be needed. But
we may need to adapt each name.

PMID: 10871379 , 10629049
-——————————————————————-
It differs from :

term: one hybrid
id: MI:0432
definition: Protein-DNA Complementation assay where a
single promoter act as bait and is screened against a
library of prey transcription factors.
definition_reference: PMID:10589421

Karine

Reported by: krobbe4

We need a parent term in controlled vocabulary for
Participant Detection which could be used for instances
where the detection method is valid but cannot be
depicted by the terms currently in the CVs or a one off
method which in itself may not be used very often, but
never the less is viable. This could also be used for
suggested terms.

Reported by: jyotikhadake

Required for PSI-MI Level 2.5 schema. Current contents

Purified

Cell lysate

Living cell

Fixed cell

cDNA library

Reported by: orchard

draft genetic method expansion:
—genetic interference
This term refers to methods that aim at interfering
with the activity of a specific gene by altering the
gene regulatory or coding sequences. This goal can be
achieved either by a classical genetic approach (random
mutagenesis followed by phenotype characterization and
genetic mapping) or by a reverse genetics approach
where a gene of interest is modified by directed
mutagenesis.
-——————-random mutagenesis
-——————synthetic genetic analysis
—expression interference
This term refers to methods designed to interfere with
gene expression rather than with the gene itself. This
class of methods are either designed to interfere with
gene transcripts or directly with their protein products.
-————————RNA interference RNAi RNA
interference (RNAi) is a post-translational gene
silencing method reproducing a naturally occurring
phenomena. RNAi is the process whereby double-stranded
RNA (dsRNA) induces the sequence-specific degradation
of homologous mRNA. RNAi or dsRNA-induced silencing
phenomena are present in evolutionarily diverse
organisms, e.g., nematodes, plants, fungi, and
trypanosomes. The mechanisms by which RNAi works is
initiated by a processive cleavage of dsRNA into 21 to
23 nucleotide (nt) short interfering RNAs (siRNAs).
These native siRNA duplexes are then incorporated into
a protein complex called RNA-induced silencing complex
(RISC). ATP-dependent unwinding of the siRNA duplex
generates an active RISC complex. Guided by the
antisense strand of siRNA, the active RISC complex
recognizes and cleaves the corresponding mRNA. 12408823
and 12110901
-———————-Antisense RNA This approach is based
on the observation that expression of RNA that is
complementary to a specific mRNA can decrease the
synthesis of its gene product either by increasing the
degradation of the targeted mRNA or by interfering with
its translation. 1340158
-———————-inhibitor Antibodies Intracellular
(or extracellular) expression of antibodies is used to
target specific gene products in order to inactivate
them. Most of the times the antibody scaffold need s to
reengineered for efficient expression and solubility in
the cytoplasm. 10189716
-————————Perturbagens peptides This approach
is based on the expression of peptides that bind to
specific target proteins thereby interfering with their
activity. In a standard approach the interfering
peptide is expressed by genetic fusion to a stable
protein scaffold. Interfering peptides can also be
introduced into cells by fusing them to proteins or
peptides (homeodomains, Tat protein�) having the
property of penetrating the cell membrane. The
peptide-carrier fusion protein is either synthesized
chemically or produced in vivo, normally in bacteria.
When the purified fusion protein is added to a cell
culture, it penetrates the cell membrane thereby
permitting the fused peptide to interfere with its
target protein. 8606778 and 11731788
-————————-Inhibitor Small molecules Protein
activity is inhibited by small inorganic molecules
(drugs) that specifically bind to their targets.
Recently this classical pharmacological approach is
sometime referred to as �chemical genetics�. 10780927
and 10542155
################################################
NOTE : such hierarchy is compatible with biopax
evidence code.
################################################
Inferred from mutant phenotype. IMP inferred from
mutant phenotype. The assertion was inferred from a
mutant phenotype such as o Any gene mutation/knockout o
Overexpression/ectopic expression of wild-type or
mutant genes o Anti-sense experiments o RNA
interference experiments o Specific protein inhibitors
Comment: Inferences made from examining mutations or
abnormal levels of only the product(s) of the gene of
interest are covered by code EV-IMP (compare to code
EV-IGI). Use this code for experiments that use
antibodies or other specific inhibitors of RNA or
protein activity, even though no gene may be mutated
(the rationale is that EV-IMP is used where an abnormal
situation prevvails in a cell or organism).

Inferred from genetic interaction. IGI inferred from
genetic interaction. The assertion was inferred from a
genetic interaction such as o “Traditional” genetic
interactions such as suppressors, synthetic lethals,
etc. o Functional complementation o Rescue experiments
o Inference about one gene drawn from the phenotype of
a mutation in a different gene This category includes
any combination of alterations in the sequence
(mutation) or expression of more than one gene/gene
product. This category can therefore cover any of the
IMP experiments that are done in a non-wild-type
background, although we prefer to use it only when all
mutations are documented. When redundant copies of a
gene must all be mutated to see an informative
phenotype, use the IGI code. (Yes, this implies some
organisms, such as mouse, will have far, far more IGI
than IMP annotations.) IMP also covers phenotypic
similarity: a phenotype that is informative because it
is similar to that of another independent phenotype
(which may have been described earlier or documented
more fully) is IMP (not IGI). We have also decided to
use this category for situations where a mutation in
one gene (gene A) provides information about the
function, process, or component of another gene (gene
B; i.e. annotate gene B using IGI).

Reported by: luisa_montecchi