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MIMIx-Excel-Workbook

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MIMIx-Excel-Workbook Powered By Docstoc
					MIMIx Data Entry Excel Workbook

http://www.ebi.ac.uk/ontology-lookup

If you wish to browse all of the available PSI-MI terms, please take a look at the (read-only) termLookup sheet.

Entering PSI-MI terms into the Interactions spreadsheet
PSI-MI terms are used in the following columns:

. Reference Database (Columns B & C) . Experiment Role (Columns H & I) . Biological Role (Columns J & K) . Interaction Detection (Columns L & M) . Participant Detection (Columns N & O)

pjones@ebi.ac.uk

MIMIx Data Entry Excel Workbook
This Excel workbook makes use of Visual Basic code to allow it to look up information related to the HUPO PSI-MI ontology. To help to ensure that the spreadsheet has not been tampered with and does not contain any viruses, it has been signed using a Thawte Digital Signature.

This workbook makes use of the Ontology Lookup Service from the EBI to obtain the most up-to-date version of the HUPO PSI-MI ontology that you can use to annotate your data. The relevant ontology terms are updated each time the spreadsheet is opened. For this to work, you need to be on-line with access to the Internet. If this is not the case, you can still use the workbook. http://www.ebi.ac.uk/ontology-lookup

When you open the spreadsheet, a dialogue box will open asking you if you wish to update the ontology. If you are working off-line, click on 'No' to continue. Updating the ontology terms takes a few seconds over the internet. A new dialogue box will then appear to inform you of update success / failure. If you wish to browse all of the available PSI-MI terms, please take a look at the (read-only) termLookup sheet.

Entering PSI-MI terms into the Interactions spreadsheet
PSI-MI terms are used in the following columns:

. Reference Database (Columns B & C) . Experiment Role (Columns H & I) . Biological Role (Columns J & K) . Interaction Detection (Columns L & M) . Participant Detection (Columns N & O)
In each case, the first column contain the ontology term accession. This column is read only. The second column contains a pull-down list of the available terms in the ontology. It is this list of available terms that is updated from the Ontology Lookup Service. To select the ontology term that you require, you can either click on the term cell (the right hand column in each case) and select the correct term from the list that is displayed, or you can type the first few letters of the term. It is also possible to paste in terms into this column, or to use Excel's built in tools for copying a single entry to multiple cells. The correct PSI-MI accession number will be entered into the left hand column automatically in either case. If you have any problems with the spreadsheet that are connected with the automated use of ontologies, please contact: pjones@ebi.ac.uk

This sheet contains details of Contacts (one minimum) that will be included in the XML file. ↓ Name ↓ Institution ↓ Email Address

Publication Title

First Author

Publication Identifier

Page Complete ↓ Status

Interactions must be numbered to group interactors. Mandatory.

The reference database for the interactors. This should normally be UniProt or RefSeq. Publicly accessible model organism databases are acceptable. Mandatory.

NCBI taxid for the Host Organism in which the interaction took place. Details of tissue or cell lines may be added as free text. Mandatory.

Primary accession number from the referenced database. Mandatory.

Interaction number

Accession

Database

Taxid

Interactor AC

Name used for the interactor in the publication, or commonly used name. Optional.

NCBI taxid for the interactor. Mandatory for protein and nucleotide sequences if reference database accession number not given. Not mandatory for small molecules. Taxid

The role of the interactor in the interaction, usually bait, prey or neutral component. Mandatory.

The biological role of the interactor in the interaction, for example enzyme, enzyme target, cofactor, unspecified role.

Interactor name

Accession Experimental Role

Accession Biological Role

Interaction detection method. See for a list of possible methods. Mandatory.

Participant detection method. See for a list of possible methods. Optional.

Other information, e.g. interacting domains, or protein tags. Optional. Other

Accession Interaction detection

Accession Participant detection

PSI-MI Ontology Terms, Retrieved from the Ontology Lookup Service
Experimental Role Accession MI:0684 MI:0496 MI:0584 MI:0583 MI:0497 MI:0498 MI:0503 MI:0582 MI:0581 MI:0499 Term ancillary bait fluorescence acceptor fluorescence donor neutral component prey self suppressed gene suppressor gene unspecified role Accession MI:0682 MI:0580 MI:0579 MI:0501 MI:0502 MI:0587 MI:0586 MI:0503 MI:0499 Biological Role

MI:0012 MI:0013 MI:0276 MI:0602 MI:0225 MI:0402 MI:0091 MI:0016 MI:0017 MI:0019 MI:0513 MI:0404 MI:0405 MI:0024 MI:0663 MI:0026 MI:0027 MI:0028 MI:0029 MI:0030 MI:0228 MI:0406 MI:0508 MI:0111 MI:0603 MI:0034 MI:0697 MI:0698 MI:0409 MI:0606 MI:0035 MI:0036 MI:0037 MI:0038 MI:0040 MI:0041

MI:0042 MI:0043 MI:0410 MI:0413 MI:0412 MI:0605 MI:0415 MI:0411 MI:0045 MI:0046 MI:0047 MI:0048 MI:0049 MI:0052 MI:0416 MI:0053 MI:0051 MI:0054 MI:0055 MI:0417 MI:0057 MI:0254 MI:0058 MI:0229 MI:0419 MI:0510 MI:0428 MI:0514 MI:0362 MI:0363 MI:0364 MI:0423 MI:0063 MI:0064 MI:0226 MI:0065 MI:0420 MI:0425 MI:0066 MI:0655 MI:0369 MI:0426 MI:0067 MI:0231 MI:0069 MI:0230 MI:0515 MI:0516 MI:0071 MI:0073 MI:0077 MI:0430 MI:0432 MI:0081 MI:0084 MI:0434

MI:0509 MI:0085 MI:0696 MI:0255 MI:0604 MI:0087 MI:0435 MI:0511 MI:0089 MI:0090 MI:0031 MI:0092 MI:0424 MI:0437 MI:0095 MI:0096 MI:0439 MI:0227 MI:0097 MI:0098 MI:0699 MI:0700 MI:0256 MI:0438 MI:0695 MI:0440 MI:0099 MI:0100 MI:0101 MI:0104 MI:0105 MI:0107 MI:0441 MI:0657 MI:0108 MI:0676 MI:0110 MI:0370 MI:0232 MI:0020 MI:0018 MI:0397 MI:0399 MI:0398 MI:0112 MI:0686 MI:0114 MI:0115 MI:0512

y Lookup Service
Biological Role Term cofactor electron acceptor electron donor enzyme enzyme target inhibited inhibitor self unspecified role

http://www.ebi.ac.uk/ontology-lookup Interaction Detection Accession MI:0588 MI:0014 MI:0004 MI:0400 MI:0006 MI:0007 MI:0678 MI:0257 MI:0008 MI:0009 MI:0010 MI:0011 MI:0401 MI:0012 MI:0013 MI:0276 MI:0602 MI:0225 MI:0402 MI:0091 MI:0016 MI:0017 MI:0019 MI:0513 MI:0404 MI:0405 MI:0024 MI:0663 MI:0026 MI:0027 MI:0028 MI:0029 MI:0030 MI:0228 MI:0406 MI:0508 MI:0111 MI:0603 MI:0034 MI:0697 MI:0698 MI:0409 MI:0606 MI:0035 MI:0036 MI:0037 MI:0038 MI:0040 MI:0041 Term 3 hybrid method adenylate cyclase complementation affinity chromatography technology affinity technology anti bait coimmunoprecipitation anti tag coimmunoprecipitation antibody array antisense rna array technology bacterial display beta galactosidase complementation beta lactamase complementation biochemical bioluminescence resonance energy transfer biophysical blue native page chemical footprinting chromatin immunoprecipitation array chromatin immunoprecipitation assays chromatography technology circular dichroism classical fluorescence spectroscopy coimmunoprecipitation collagen film assay comigration in non denaturing gel electrophoresis competition binding confirmational text mining confocal microscopy correlated mutations cosedimentation cosedimentation in solution cosedimentation through density gradient cross-linking study cytoplasmic complementation assay deacetylase assay deacetylase radiometric assay dihydrofolate reductase reconstruction dimethylsulphate footprinting display technology dna directed dna polymerase assay dna directed rna polymerase assay dna footprinting DNase I footprinting docking domain fusion domain profile pairs dynamic light scattering electron microscopy electron nuclear double resonance

MI:0042 MI:0043 MI:0410 MI:0413 MI:0412 MI:0605 MI:0415 MI:0411 MI:0045 MI:0046 MI:0047 MI:0048 MI:0049 MI:0052 MI:0416 MI:0053 MI:0051 MI:0054 MI:0055 MI:0417 MI:0057 MI:0254 MI:0058 MI:0229 MI:0419 MI:0510 MI:0428 MI:0514 MI:0362 MI:0363 MI:0364 MI:0423 MI:0063 MI:0064 MI:0226 MI:0065 MI:0420 MI:0425 MI:0066 MI:0655 MI:0369 MI:0426 MI:0067 MI:0231 MI:0069 MI:0230 MI:0515 MI:0516 MI:0071 MI:0073 MI:0077 MI:0430 MI:0432 MI:0081 MI:0084 MI:0434

electron paramagnetic resonance electron resonance electron tomography electrophoretic mobility shift assay electrophoretic mobility supershift assay enzymatic footprinting enzymatic study enzyme linked immunosorbent assay experimental interaction detection experimental knowledge based far western blotting filamentous phage display filter binding fluorescence correlation spectroscopy fluorescence microscopy fluorescence polarization spectroscopy fluorescence technology fluorescence-activated cell sorting fluorescent resonance energy transfer footprinting gene neighbourhood genetic interference genome based prediction green fluorescence protein complementation assay gtpase assay homogeneous time resolved fluorescence imaging techniques in gel phosphatase assay inference inferred by author inferred by curator in-gel kinase assay interaction prediction interologs mapping ion exchange chromatography isothermal titration calorimetry kinase homogeneous time resolved fluorescence kinase scintillation proximity assay lambda phage display lambda repressor two hybrid lex-a dimerization assay light microscopy light scattering mammalian protein protein interaction trap mass spectrometry studies of complexes membrane bound complementation assay methyltransferase assay methyltransferase radiometric assay molecular sieving mrna display nuclear magnetic resonance nucleic acid uv cross-linking assay one hybrid peptide array phage display phosphatase assay

MI:0509 MI:0085 MI:0696 MI:0255 MI:0604 MI:0087 MI:0435 MI:0511 MI:0089 MI:0090 MI:0031 MI:0092 MI:0424 MI:0437 MI:0095 MI:0096 MI:0439 MI:0227 MI:0097 MI:0098 MI:0699 MI:0700 MI:0256 MI:0438 MI:0695 MI:0440 MI:0099 MI:0100 MI:0101 MI:0104 MI:0105 MI:0107 MI:0441 MI:0657 MI:0108 MI:0676 MI:0110 MI:0370 MI:0232 MI:0020 MI:0018 MI:0397 MI:0399 MI:0398 MI:0112 MI:0686 MI:0114 MI:0115 MI:0512

phosphatase homogeneous time resolved fluorescence phylogenetic profile polymerase assay post transcriptional interference potassium permanganate footprinting predictive text mining protease assay protease homogeneous time resolved fluorescence protein array protein complementation assay protein cross-linking with a bifunctional reagent protein in situ array protein kinase assay protein tri hybrid proteinchip(r) on a surface-enhanced laser desorption/ionization pull down random spore analysis reverse phase chromatography reverse ras recruitment system ribosome display rna directed dna polymerase assay rna directed rna polymerase assay rna interference rna tri hybrid sandwich immunoassay saturation binding scintillation proximity assay sequence based phylogenetic profile sequence based prediction static light scattering structure based prediction surface plasmon resonance synthetic genetic analysis systematic evolution of ligands by exponential enrichment t7 phage display tandem affinity purification text mining tox-r dimerization assay transcriptional complementation assay transmission electron microscopy two hybrid two hybrid array two hybrid fragment pooling approach two hybrid pooling approach ubiquitin reconstruction unspecified method x-ray crystallography yeast display zymography

Participant Detection Accession MI:0707 MI:0705 MI:0032 MI:0039 MI:0411 MI:0661 MI:0056 MI:0421 MI:0422 MI:0362 MI:0363 MI:0364 MI:0427 MI:0708 MI:0072 MI:0658 MI:0078 MI:0080 MI:0433 MI:0082 MI:0083 MI:0709 MI:0086 MI:0396 MI:0088 MI:0093 MI:0102 MI:0103 MI:0113

Protein Sequence Database

Term Accession anti tag immunostaining MI:0464 anti tag western blot MI:0475 de novo protein sequencing MI:0476 spectrometry by mass edman degradation MI:0477 enzyme linked immunosorbent assay MI:0478 experimental participant identification MI:0249 full identification by sequencing MI:0675 identification by antibody MI:0479 immunostaining MI:0480 inference MI:0481 inferred by author MI:0482 inferred by curator MI:0483 mass spectrometry MI:0484 monoclonal antibody immunostaining MI:0485 monoclonal antibody western blot MI:0486 multidimensional protein identification technology MI:0487 nucleotide sequence identification partial dna sequence identification by hybridization partial identification of protein sequence peptide massfingerprinting peptide synthesis polyclonal antibody immunostaining polyclonal antibody western blot predetermined participant primer specific pcr protein sequence identification sequence tag identification southern blot western blot

imentation through density gradient

asmic complementation assay

tylase radiometric assay ofolate reductase reconstruction hylsulphate footprinting

rected dna polymerase assay rected rna polymerase assay

on nuclear double resonance

on paramagnetic resonance

ophoretic mobility shift assay ophoretic mobility supershift assay

me linked immunosorbent assay mental interaction detection mental knowledge based

scence correlation spectroscopy

scence polarization spectroscopy

scence-activated cell sorting scent resonance energy transfer

fluorescence protein complementation assay

geneous time resolved fluorescence

change chromatography rmal titration calorimetry e homogeneous time resolved fluorescence e scintillation proximity assay

a repressor two hybrid

malian protein protein interaction trap spectrometry studies of complexes rane bound complementation assay

ltransferase radiometric assay

ar magnetic resonance c acid uv cross-linking assay

hatase homogeneous time resolved fluorescence

anscriptional interference sium permanganate footprinting

se homogeneous time resolved fluorescence

n complementation assay n cross-linking with a bifunctional reagent

nchip(r) on a surface-enhanced laser desorption/ionization

e phase chromatography e ras recruitment system

ected dna polymerase assay ected rna polymerase assay

nce based phylogenetic profile

e plasmon resonance

matic evolution of ligands by exponential enrichment

riptional complementation assay mission electron microscopy

brid fragment pooling approach brid pooling approach

Protein Sequence Database Term cygd ddbj/embl/genbank ensembl entrez gene/locuslink flybase huge international protein index mgd/mgi omim refseq rfam rgd sgd uniparc uniprot knowledge base wormbase


				
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Description: MIMIx-Excel-Workbook