User:Lindenb/Notebook/UMR915/20100907
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
- Notebook
- ATP binding
- Enzyme binding
- Identical protein binding
- Kinase activity
- Nitric-oxide synthase regulator activity
- Nucleotide binding
- Phosphatidylinositol-3,4,5-trisphosphate binding
- Phosphatidylinositol-3,4-bisphosphate binding
- Protein binding
- Protein kinase activity
- Protein serine/threonine kinase activity
- Transferase activity
- G-protein coupled receptor protein signaling pathway
- Activation of pro-apoptotic gene products
- Activation-induced cell death of T cells
- Anagen
- Anti-apoptosis
- Apoptotic mitochondrial changes
- Carbohydrate metabolic process
- Carbohydrate transport
- Cell projection organization
- Cellular response to insulin stimulus
- Germ cell development
- Glucose transport
- Glycogen cell development involved in embryonic placenta development
- Inflammatory response
- Insulin receptor signaling pathway
- Insulin-like growth factor receptor signaling pathway
- Intracellular signaling pathway
- Labyrinthine layer blood vessel development
- Maternal placenta development
- Negative regulation of JNK cascade
- Negative regulation of apoptosis
- Negative regulation of cell size
- Negative regulation of fatty acid beta-oxidation
- Negative regulation of plasma membrane long-chain fatty acid transport
- Negative regulation of protein kinase activity
- Nervous system development
- Nitric oxide biosynthetic process
- Peptidyl-serine phosphorylation
- Positive regulation of cell growth
- Positive regulation of cellular protein metabolic process
- Positive regulation of cyclin-dependent protein kinase activity involved in G1/S
- Positive regulation of establishment of protein localization in plasma membrane
- Positive regulation of fat cell differentiation
- Positive regulation of glucose import
- Positive regulation of glucose metabolic process
- Positive regulation of glycogen biosynthetic process
- Positive regulation of lipid biosynthetic process
- Positive regulation of nitric oxide biosynthetic process
- Positive regulation of nitric-oxide synthase activity
- Positive regulation of proteasomal ubiquitin-dependent protein catabolic process
- Positive regulation of sodium ion transport
- Protein amino acid autophosphorylation
- Protein amino acid phosphorylation
- Protein catabolic process
- Protein import into nucleus, translocation
- Protein kinase B signaling cascade
- Protein modification process
- Protein ubiquitination
- Regulation of cell migration
- Regulation of glycogen biosynthetic process
- Regulation of neuron projection development
- Regulation of protein localization
- Regulation of survival gene product expression
- Regulation of translation
- Response to UV-A
- Response to fluid shear stress
- Response to food
- Response to heat
- Response to hormone stimulus
- Signal transduction
- Cytoplasm
- Cytosol
- Lamellipodium
- Microtubule cytoskeleton
- Nucleoplasm
- Nucleus
- Plasma membrane
- Soluble fraction
- Spindle