User:Lindenb/Notebook/UMR915/20100907

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Contents

building local gene wiki with maven

 mvn archetype:generate -DgroupId=org.lindenb.localgenemw -DartifactId=localgenewiki \
        -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false

result is:

 localgenewiki/src/main/java/org/lindenb/localgenemw/App.java
 localgenewiki/src/test/java/org/lindenb/localgenemw/AppTest.java
 localgenewiki/pom.xml


initial content of pom.xml

 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.lindenb.localgenemw</groupId>
   <artifactId>localgenewiki</artifactId>
   <packaging>jar</packaging>
   <version>1.0-SNAPSHOT</version>
   <name>localgenewiki</name>
   <url>http://maven.apache.org</url>
   <dependencies>
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
       <version>3.8.1</version>
       <scope>test</scope>
     </dependency>
   </dependencies>
 </project>

problem, i need my sources from a non-maven project (JSON parsing), or may be should I look for a json archetype ?

commited source to github: http://github.com/lindenb/mw4bio

Second test for local ncbi gene

NCBI GeneID
207
Official Symbol
AKT1

Full Name
v-akt murine thymoma viral oncogene homolog 1
Location
14q32.32
Related

HGNC:391 MIM:164730
Other Names
AKT, PKB, RAC, PRKBA, MGC99656, PKB-ALPHA, RAC-ALPHA
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

AKT1

“The serine-threonine protein kinase encoded by the AKT1 gene is catalytically inactive in serum-starved primary and immortalized fibroblasts. AKT1 and the related AKT2 are activated by platelet-derived growth factor. The activation is rapid and specific, and it is abrogated by mutations in the pleckstrin homology domain of AKT1. It was shown that the activation occurs through phosphatidylinositol 3-kinase. In the developing nervous system AKT is a critical mediator of growth factor-induced neuronal survival. Survival factors can suppress apoptosis in a transcription-independent manner by activating the serine/threonine kinase AKT1, which then phosphorylates and inactivates components of the apoptotic machinery. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq]”

Interactions

AHNAK, AKT1, AKT1S1, AKT2, AKTIP, AKTIP, APLP2, APPL1, APPL1, AR, AR, AR, ARFIP2, ARHGAP29, ARHGAP32, ATXN1, Akt2, BAD, BAD, BCL10, BCL2L11, BRAF, BRAF, BRCA1, BRCA1, CAMKK1, CARHSP1, CASP3, CASP9, CCDC88A, CDKN1A, CDKN1B, CDKN1B, CHEK1, CHN2, CHUK, CHUK, CREB1, CSNK2A1, DLC1, EIF4EBP1, EP300, ESR1, ESR2, EZH2, FANCA, FANCA, FOXO1, FOXO3, FOXO4, FOXO4, GAB2, GAB2, GATA1, GATA2, GRB10, GSK3A, GSK3B, GSK3B, GSK3B, HIST2H2BE, HMOX1, HSP90AA1, HSP90AA1, HSP90AB1, HSP90AB1, HSPB1, HTT, HTT, IKBKB, ILK, ILK, ILK, IMPDH2, IMPDH2, IMPDH2, IRAK1, IRAK1, IRS1, IRS1, ITGB3, KRT10, KRT10, KTN1, MAP2K4, MAP2K4, MAP3K11, MAP3K11, MAP3K5, MAP3K8, MAP3K8, MAPK14, MAPK8IP1, MAPK8IP1, MAPKAP1, MAPKAPK2, MAPKAPK2, MARK2, MDM2, MDM2, MDM4, METTL1, METTL1, MS4A2, MST1R, MTCP1, MTCP1, MTOR, MTOR, NCF1, NCF1C, NF2, NOS3, NPM1, NR4A1, NR4A1, PAK1, PAK1, PAK6, PDE3B, PDK1, PDK2, PDPK1, PDPK1, PDPK1, PEA15, PEA15, PFKFB2, PHB2, PHLPP1, PIAS1, PIAS2, PIAS2, PIK3R1, PKN2, PKN2, PLXNA1, PLXNA1, PLXNB1, PPARGC1B, PPL, PPM1A, PPP2CA, PRG2, PRKCQ, PRKCQ, PRKCZ, PRKCZ, PRKDC, PRKDC, PTEN, PTPN1, RAB3D, RAC1, RAF1, RAF1, RHEBL1, RICTOR, RPS6KB1, RPS6KB1, S1PR1, SH2B2, SMAD2, SMAD2, SMAD3, SMAD3, SMAD4, SMAD4, SMAD7, SMAD7, SORBS2, SRC, STAT1, STUB1, TCL1A, TCL1A, TCL1A, TCL1B, TCL1B, TCL1B, TERT, TERT, THEM4, THEM4, TNFSF11, TOPBP1, TRIB3, TRIB3, TSC1, TSC1, TSC2, TSC2, TSC2, UBC, USP8, UXS1, VEGFA, WNK1, XIAP, YAP1, YBX1, YBX1, YWHAZ, YWHAZ, YWHAZ and YWHAZ

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