{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Introduction to _py2cytoscape_: Pythonista-friendly wrapper for cyREST\n", "\n", "![](http://cl.ly/XohP/logo300.png)\n", "\n", "
\n", " | alias | \n", "annotation.DB_Object_Name | \n", "annotation.GO BIOLOGICAL_PROCESS | \n", "annotation.GO CELLULAR_COMPONENT | \n", "annotation.GO MOLECULAR_FUNCTION | \n", "label | \n", "kegg | \n", "uniprot | \n", "sgd | \n", "entrez | \n", "
---|---|---|---|---|---|---|---|---|---|---|
YAL003W | \n", "translation elongation factor EF-1beta, EF-1 b... | \n", "EF-1 beta, translation elongation factor EF-1beta | \n", "translational elongation | \n", "eukaryotic translation elongation factor 1 com... | \n", "translation elongation factor activity | \n", "EF1B | \n", "sce:YAL003W | \n", "EF1B_YEAST | \n", "S000000003 | \n", "851260 | \n", "
YAL030W | \n", "S000000028, SNC1 | \n", "NaN | \n", "Golgi to plasma membrane transport, endocytosi... | \n", "Golgi trans face, SNARE complex, endosome, tra... | \n", "v-SNARE activity | \n", "SNC1 | \n", "sce:YAL030W | \n", "SNC1_YEAST | \n", "S000000028 | \n", "851203 | \n", "
YAL038W | \n", "CDC19, PYK1, S000000036, pyruvate kinase | \n", "pyruvate kinase | \n", "glycolysis, pyruvate metabolic process | \n", "cytosol | \n", "pyruvate kinase activity | \n", "KPYK1 | \n", "sce:YAL038W | \n", "KPYK1_YEAST | \n", "S000000036 | \n", "851193 | \n", "
YAL040C | \n", "CLN3, DAF1, FUN10, G1 cyclin, S000000038, WHI1 | \n", "G1 cyclin | \n", "G1/S transition of mitotic cell cycle, regulat... | \n", "nucleus | \n", "cyclin-dependent protein kinase regulator acti... | \n", "CG13 | \n", "sce:YAL040C | \n", "CG13_YEAST | \n", "S000000038 | \n", "851191 | \n", "
YAR007C | \n", "heterotrimeric RPA (RF-A) single-stranded DNA ... | \n", "RF-A, heterotrimeric RPA (RF-A) single-strande... | \n", "DNA recombination, DNA replication, synthesis ... | \n", "DNA replication factor A complex, chromosome, ... | \n", "damaged DNA binding, single-stranded DNA binding | \n", "RFA1 | \n", "sce:YAR007C | \n", "RFA1_YEAST | \n", "S000000065 | \n", "851266 | \n", "
\n", " | CyNetwork | \n", "
---|---|
file:////Users/kono/git/py2cytoscape/examples/sample_yeast_network.xgmml | \n", "<py2cytoscape.data.cynetwork.CyNetwork object ... | \n", "
http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif | \n", "<py2cytoscape.data.cynetwork.CyNetwork object ... | \n", "
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/brca1?format=xml25 | \n", "<py2cytoscape.data.cynetwork.CyNetwork object ... | \n", "
\n", " | source | \n", "interaction | \n", "target | \n", "
---|---|---|---|
0 | \n", "YKR026C | \n", "pp | \n", "YGL122C | \n", "
1 | \n", "YGR218W | \n", "pp | \n", "YGL097W | \n", "
2 | \n", "YGL097W | \n", "pp | \n", "YOR204W | \n", "
3 | \n", "YLR249W | \n", "pp | \n", "YPR080W | \n", "
4 | \n", "YLR249W | \n", "pp | \n", "YBR118W | \n", "
\n", " | #ID(s) interactor A | \n", "ID(s) interactor B | \n", "Alt. ID(s) interactor A | \n", "Alt. ID(s) interactor B | \n", "Alias(es) interactor A | \n", "Alias(es) interactor B | \n", "Interaction detection method(s) | \n", "Publication 1st author(s) | \n", "Publication Identifier(s) | \n", "Taxid interactor A | \n", "... | \n", "Checksum(s) interactor A | \n", "Checksum(s) interactor B | \n", "Interaction Checksum(s) | \n", "Negative | \n", "Feature(s) interactor A | \n", "Feature(s) interactor B | \n", "Stoichiometry(s) interactor A | \n", "Stoichiometry(s) interactor B | \n", "Identification method participant A | \n", "Identification method participant B | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "uniprotkb:Q8IZC7 | \n", "uniprotkb:P11802 | \n", "intact:EBI-5278328|uniprotkb:C9JU83|uniprotkb:... | \n", "intact:EBI-295644|uniprotkb:B2R9A0|uniprotkb:B... | \n", "psi-mi:zn101_human(display_long)|uniprotkb:ZNF... | \n", "psi-mi:cdk4_human(display_long)|uniprotkb:CDK4... | \n", "psi-mi:\"MI:0424\"(protein kinase assay) | \n", "Anders et al. (2011) | \n", "pubmed:22094256|imex:IM-16628 | \n", "taxid:9606(human)|taxid:9606(Homo sapiens) | \n", "... | \n", "rogid:mZLXs/PbWbfgLzkjwZfoE2c6jy09606 | \n", "rogid:pxIzF9EkX+gMz7zj/TDiytYtsOc9606 | \n", "intact-crc:0486DE729E5A8158|rigid:3gdrHm0coV8S... | \n", "False | \n", "glutathione s tranferase tag:?-? | \n", "sufficient binding region:4-303|glutathione s ... | \n", "- | \n", "- | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "
1 | \n", "uniprotkb:P01106 | \n", "uniprotkb:Q00534 | \n", "intact:EBI-447544|intact:EBI-1058440|uniprotkb... | \n", "intact:EBI-295663|uniprotkb:A4D1G0 | \n", "psi-mi:myc_human(display_long)|uniprotkb:BHLHE... | \n", "psi-mi:cdk6_human(display_long)|uniprotkb:CDK6... | \n", "psi-mi:\"MI:0424\"(protein kinase assay) | \n", "Anders et al. (2011) | \n", "pubmed:22094256|imex:IM-16628 | \n", "taxid:9606(human)|taxid:9606(Homo sapiens) | \n", "... | \n", "rogid:CCk+p9FN7JV6cTmJDlin2hRp1tg9606 | \n", "rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606 | \n", "intact-crc:20A3DCC8419B269E|rigid:bfSR2lJKa/lY... | \n", "False | \n", "glutathione s tranferase tag:?-? | \n", "his tag:n-n | \n", "- | \n", "- | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "
2 | \n", "uniprotkb:Q00534 | \n", "uniprotkb:P28698 | \n", "intact:EBI-295663|uniprotkb:A4D1G0 | \n", "intact:EBI-5278283|uniprotkb:M0QXU0|uniprotkb:... | \n", "psi-mi:cdk6_human(display_long)|uniprotkb:CDK6... | \n", "psi-mi:mzf1_human(display_long)|uniprotkb:MZF1... | \n", "psi-mi:\"MI:0424\"(protein kinase assay) | \n", "Anders et al. (2011) | \n", "pubmed:22094256|imex:IM-16628 | \n", "taxid:9606(human)|taxid:9606(Homo sapiens) | \n", "... | \n", "rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606 | \n", "rogid:1rq+ga/Uew705r63KlORpqBObbw9606 | \n", "intact-crc:578214FA683591D0|rigid:8AADqx3NNAXF... | \n", "False | \n", "his tag:n-n | \n", "glutathione s tranferase tag:?-? | \n", "- | \n", "- | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "
3 | \n", "uniprotkb:P11802 | \n", "uniprotkb:Q9H165 | \n", "intact:EBI-295644|uniprotkb:B2R9A0|uniprotkb:B... | \n", "intact:EBI-765567|uniprotkb:Q86W14|uniprotkb:Q... | \n", "psi-mi:cdk4_human(display_long)|uniprotkb:CDK4... | \n", "psi-mi:bc11a_human(display_long)|uniprotkb:B-c... | \n", "psi-mi:\"MI:0424\"(protein kinase assay) | \n", "Anders et al. (2011) | \n", "pubmed:22094256|imex:IM-16628 | \n", "taxid:9606(human)|taxid:9606(Homo sapiens) | \n", "... | \n", "rogid:pxIzF9EkX+gMz7zj/TDiytYtsOc9606 | \n", "rogid:xASsLQWykg/7ZpyjLsQP8GlQ/H09606 | \n", "intact-crc:F173ABFF34E61592|rigid:5u6F7IwnpEEf... | \n", "False | \n", "sufficient binding region:4-303|glutathione s ... | \n", "glutathione s tranferase tag:?-? | \n", "- | \n", "- | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "
4 | \n", "uniprotkb:Q14980 | \n", "uniprotkb:Q00534 | \n", "intact:EBI-521611|uniprotkb:H0YH75|uniprotkb:Q... | \n", "intact:EBI-295663|uniprotkb:A4D1G0 | \n", "psi-mi:numa1_human(display_long)|uniprotkb:SP-... | \n", "psi-mi:cdk6_human(display_long)|uniprotkb:CDK6... | \n", "psi-mi:\"MI:0424\"(protein kinase assay) | \n", "Anders et al. (2011) | \n", "pubmed:22094256|imex:IM-16628 | \n", "taxid:9606(human)|taxid:9606(Homo sapiens) | \n", "... | \n", "rogid:goAKbcTz6vzGy3T7RlpGPnTCbdk9606 | \n", "rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606 | \n", "intact-crc:43D7B9AE4E55FAA0|rigid:mLhZxkGnjrpK... | \n", "False | \n", "glutathione s tranferase tag:?-? | \n", "his tag:n-n | \n", "- | \n", "- | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "psi-mi:\"MI:0821\"(molecular weight estimation b... | \n", "
5 rows × 42 columns
\n", "\n", " | source | \n", "interaction | \n", "target | \n", "
---|---|---|---|
0 | \n", "YDR277C | \n", "pp | \n", "YDL194W | \n", "
1 | \n", "YDR277C | \n", "pp | \n", "YJR022W | \n", "
2 | \n", "YPR145W | \n", "pp | \n", "YMR117C | \n", "
3 | \n", "YER054C | \n", "pp | \n", "YBR045C | \n", "
4 | \n", "YER054C | \n", "pp | \n", "YER133W | \n", "
\n", " | shared name | \n", "name | \n", "selected | \n", "id | \n", "Degree | \n", "Betweenness_Centrality | \n", "
---|---|---|---|---|---|---|
SUID | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
248218 | \n", "0 | \n", "0 | \n", "False | \n", "0 | \n", "63 | \n", "0.032124 | \n", "
248219 | \n", "1 | \n", "1 | \n", "False | \n", "1 | \n", "94 | \n", "0.085927 | \n", "
248220 | \n", "2 | \n", "2 | \n", "False | \n", "2 | \n", "24 | \n", "0.013760 | \n", "
248221 | \n", "3 | \n", "3 | \n", "False | \n", "3 | \n", "7 | \n", "0.000000 | \n", "
248222 | \n", "4 | \n", "4 | \n", "False | \n", "4 | \n", "13 | \n", "0.016595 | \n", "
SUID | \n", "248208 | \n", "
---|---|
shared name | \n", "directed_scale_free_graph(100,alpha=0.41,beta=... | \n", "
name | \n", "directed_scale_free_graph(100,alpha=0.41,beta=... | \n", "
selected | \n", "True | \n", "
__Annotations | \n", "NaN | \n", "
\n", " | immutable | \n", "primaryKey | \n", "type | \n", "
---|---|---|---|
name | \n", "\n", " | \n", " | \n", " |
SUID | \n", "True | \n", "True | \n", "Long | \n", "
shared name | \n", "True | \n", "False | \n", "String | \n", "
name | \n", "True | \n", "False | \n", "String | \n", "
selected | \n", "True | \n", "False | \n", "Boolean | \n", "
id | \n", "False | \n", "False | \n", "String | \n", "
Degree | \n", "False | \n", "False | \n", "Double | \n", "
Betweenness_Centrality | \n", "False | \n", "False | \n", "Double | \n", "
\n", " | source | \n", "target | \n", "
---|---|---|
SUID | \n", "\n", " | \n", " |
248820 | \n", "248814 | \n", "248815 | \n", "
248821 | \n", "248814 | \n", "248816 | \n", "
248822 | \n", "248815 | \n", "248816 | \n", "
\n", " | kegg | \n", "uniprot | \n", "sgd | \n", "entrez | \n", "name | \n", "
---|---|---|---|---|---|
0 | \n", "sce:YKR026C | \n", "EI2BA_YEAST | \n", "S000001734 | \n", "853896 | \n", "YKR026C | \n", "
1 | \n", "sce:YGL122C | \n", "NAB2_YEAST | \n", "S000003090 | \n", "852755 | \n", "YGL122C | \n", "
2 | \n", "sce:YGR218W | \n", "XPO1_YEAST | \n", "S000003450 | \n", "853133 | \n", "YGR218W | \n", "
3 | \n", "sce:YGL097W | \n", "RCC1_YEAST | \n", "S000003065 | \n", "852782 | \n", "YGL097W | \n", "
4 | \n", "sce:YOR204W | \n", "DED1_YEAST | \n", "S000005730 | \n", "854379 | \n", "YOR204W | \n", "
\n", " | shared name | \n", "name | \n", "selected | \n", "id | \n", "foo | \n", "kegg | \n", "entrez | \n", "uniprot | \n", "sgd | \n", "
---|---|---|---|---|---|---|---|---|---|
SUID | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
246470 | \n", "YKR026C | \n", "YKR026C | \n", "False | \n", "YKR026C | \n", "NaN | \n", "sce:YKR026C | \n", "853896 | \n", "EI2BA_YEAST | \n", "S000001734 | \n", "
246471 | \n", "YGL122C | \n", "YGL122C | \n", "False | \n", "YGL122C | \n", "NaN | \n", "sce:YGL122C | \n", "852755 | \n", "NAB2_YEAST | \n", "S000003090 | \n", "
246472 | \n", "YGR218W | \n", "YGR218W | \n", "False | \n", "YGR218W | \n", "NaN | \n", "sce:YGR218W | \n", "853133 | \n", "XPO1_YEAST | \n", "S000003450 | \n", "
246473 | \n", "YGL097W | \n", "YGL097W | \n", "False | \n", "YGL097W | \n", "NaN | \n", "sce:YGL097W | \n", "852782 | \n", "RCC1_YEAST | \n", "S000003065 | \n", "
246474 | \n", "YOR204W | \n", "YOR204W | \n", "False | \n", "YOR204W | \n", "NaN | \n", "sce:YOR204W | \n", "854379 | \n", "DED1_YEAST | \n", "S000005730 | \n", "
\n", " | shared name | \n", "name | \n", "selected | \n", "id | \n", "foo | \n", "entrez | \n", "uniprot | \n", "sgd | \n", "New Empty Double Column | \n", "Empty String Col | \n", "
---|---|---|---|---|---|---|---|---|---|---|
SUID | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
246470 | \n", "YKR026C | \n", "YKR026C | \n", "False | \n", "YKR026C | \n", "NaN | \n", "853896 | \n", "EI2BA_YEAST | \n", "S000001734 | \n", "NaN | \n", "NaN | \n", "
246471 | \n", "YGL122C | \n", "YGL122C | \n", "False | \n", "YGL122C | \n", "NaN | \n", "852755 | \n", "NAB2_YEAST | \n", "S000003090 | \n", "NaN | \n", "NaN | \n", "
246472 | \n", "YGR218W | \n", "YGR218W | \n", "False | \n", "YGR218W | \n", "NaN | \n", "853133 | \n", "XPO1_YEAST | \n", "S000003450 | \n", "NaN | \n", "NaN | \n", "
246473 | \n", "YGL097W | \n", "YGL097W | \n", "False | \n", "YGL097W | \n", "NaN | \n", "852782 | \n", "RCC1_YEAST | \n", "S000003065 | \n", "NaN | \n", "NaN | \n", "
246474 | \n", "YOR204W | \n", "YOR204W | \n", "False | \n", "YOR204W | \n", "NaN | \n", "854379 | \n", "DED1_YEAST | \n", "S000005730 | \n", "NaN | \n", "NaN | \n", "
\n", " | data | \n", "position | \n", "selected | \n", "
---|---|---|---|
0 | \n", "{'sgd': 'S000002353', 'name': 'YDL194W', 'sele... | \n", "{'y': 337.3408049125783, 'x': -816.2080368805437} | \n", "False | \n", "
1 | \n", "{'sgd': 'S000002685', 'name': 'YDR277C', 'sele... | \n", "{'y': 283.5470442679916, 'x': -768.351675592697} | \n", "False | \n", "
2 | \n", "{'sgd': 'S000000247', 'name': 'YBR043C', 'sele... | \n", "{'y': 700.0122446801881, 'x': 166.44780103059588} | \n", "False | \n", "
3 | \n", "{'sgd': 'S000006349', 'name': 'YPR145W', 'sele... | \n", "{'y': 549.1767770841686, 'x': -524.6571716355409} | \n", "False | \n", "
4 | \n", "{'sgd': 'S000000856', 'name': 'YER054C', 'sele... | \n", "{'y': -104.59739351311714, 'x': 1446.504571276... | \n", "False | \n", "