Code |
Context $json = $this->create_JSON($id, '___');
} else {
$json = $this->create_JSON($target_id, '___');
$target_id = "006146"
$split = "___"
$target = array(
"Target" => array(
"id" => "10675",
"target_id" => "006146",
"local_target_id" => "006146",
"locus_tag" => null,
"ncbi_gi" => "81867099",
"ncbi_accession" => "Q8VBT3.1",
"ncbi_geneid" => null,
"ncbi_taxon_id" => "10090",
"gene_name" => "Oscar",
"common_name" => "RecName: Full=Osteoclast-associated immunoglobulin-like receptor; Short=Osteoclast-associated receptor; Short=mOSCAR; AltName: Full=Ocl178; Flags: Precursor",
"ncbi_coded_by_region" => null,
"ncbi_note" => null,
"tigr_main_role_id" => null,
"tigr_sub_role_id" => null,
"comment" => null,
"justification" => " Structural genomics of cell surface anchored Immunoglobulin Superfamily proteins that mediate immune response of T cells; human proteins and their orthologs",
"sequence" => "MVLSLILQLSTLWPACRADFTPTAPLASYPQPWLGAHPAAVVTPGINVTLTCRAPQSAWRFALFKSGLVTPLLLRDVSVELAEFFLEEVTPAQGGSYHCRYRKTDWGPGVWSQPSNVLELLVTDQLPRPSLVALPGPVVAPGANVSLRCAGRIPGMSFALYRVGVATPLQYIDSVQPWADFLLIGTHTPGTYCCYYHTPSAPYVLSQRSQPLVISFEGSGSLDYTQGNLIRLGLAGMVLICLGIIVTCDWHSRSSAFDGLLPQQN",
"sequence_length" => "265",
"dna_sequence" => "ATGGTCCTGTCGCTGATACTCCAGCTGTCGACTCTCTGGCCTGCATGCCGTGCTGACTTCACACCAACAGCGCCCCTAGCCTCATACCCCCAGCCATGGCTGGGAGCTCATCCTGCTGCAGTTGTGACTCCTGGGATCAACGTGACCTTGACTTGCCGCGCACCTCAATCTGCCTGGCGGTTTGCACTCTTCAAAAGTGGCCTTGTCACCCCTCTGCTCCTCCGGGATGTGTCCGTTGAGCTGGCTGAGTTCTTCCTGGAAGAAGTGACTCCGGCCCAAGGGGGCAGTTATCACTGCCGCTACCGCAAGACAGACTGGGGGCCAGGTGTCTGGTCTCAGCCCAGTAATGTTCTGGAACTGCTGGTAACGGATCAGCTCCCCAGACCATCACTGGTGGCACTGCCTGGGCCTGTGGTGGCCCCGGGAGCCAACGTAAGCCTGCGCTGTGCAGGCCGCATACCGGGCATGAGTTTTGCACTGTACCGCGTAGGCGTGGCAACCCCTCTGCAGTATATTGACTCTGTGCAGCCCTGGGCTGACTTCCTTTTGATCGGCACACACACACCTGGCACCTACTGTTGCTATTACCACACGCCTTCTGCCCCCTATGTGCTATCACAGCGCAGCCAGCCACTGGTCATCAGTTTCGAAGGTTCTGGCTCCTTGGACTATACCCAGGGAAACCTCATCCGTTTGGGGCTGGCAGGAATGGTCCTCATCTGCTTGGGCATCATAGTTACTTGTGATTGGCACAGCAGGAGCTCTGCCTTTGATGGTCTCCTGCCCCAGCAAAACTGA",
"dna_sequence_ncbi" => null,
"priority" => "1",
"project" => "IFN:IgSF (Immune Function Network)",
"selection_phase" => null,
"date_selected" => "2011-01-20",
"date_approved" => "2011-02-10",
"completion_code" => null,
"pi" => null,
"tms" => null,
"sp" => null,
"core_genome" => null,
"gram_minus_gene_homolog" => null,
"gram_plus_gene_homolog" => null,
"protease_motifs" => null,
"glycosyl_group_metabolism" => null,
"study_id" => null,
"drug_target_homologs" => null,
"virulence_genes" => null,
"essential_genes_homologs" => null,
"dna_binding_motifs" => null,
"inserted" => "2011-02-10 18:45:56.060701+00",
"updated" => "2011-02-10 18:45:56.060701+00",
"species_taxon_id" => "10090",
"ins_user_id" => "2",
"upd_user_id" => null,
"stage" => "in_crystallization_trials",
"hidden" => false,
"submitter_id" => null,
"selection_db_id" => null,
"dna_source_taxon_id" => null,
"batch" => null,
"genus_taxon_id" => "10088",
"seguid" => null,
"uniprot_id" => null,
"ec" => null,
"target_family" => null,
"tar_designpool_id" => null,
"community_nominated" => false,
"partnership_nominated" => "IFN",
"biomedical" => false,
"metagenomic" => false,
"structural_coverage" => false,
"psi2" => false,
"legacy" => false,
"complex_with_biological_partner" => false,
"functional_mutant" => false,
"conformational_state" => false,
"disease" => false,
"individual_organism" => false,
"protein_family_of_high_biological_importance" => false,
"general_domain_family" => false,
"eukaryotic_domain_family" => false,
"first_structure_of_class" => false,
"functional_follow_up" => false,
"technology_development" => false,
"membrane_protein" => false,
"translated_dna_sequence" => "MVLSLILQLSTLWPACRADFTPTAPLASYPQPWLGAHPAAVVTPGINVTLTCRAPQSAWRFALFKSGLVTPLLLRDVSVELAEFFLEEVTPAQGGSYHCRYRKTDWGPGVWSQPSNVLELLVTDQLPRPSLVALPGPVVAPGANVSLRCAGRIPGMSFALYRVGVATPLQYIDSVQPWADFLLIGTHTPGTYCCYYHTPSAPYVLSQRSQPLVISFEGSGSLDYTQGNLIRLGLAGMVLICLGIIVTCDWHSRSSAFDGLLPQQN",
"family_coverage" => null,
"family_coverage_date" => null,
"distribution_lab" => null,
"uniprot_accession" => null,
"protocol_id" => "Target_selection",
"ensembl_protein_id" => null,
"ensembl_gene_id" => null,
"type" => "single protein",
"ligand_studies" => false,
"protein_production_for_partnerships" => false,
"single_domain_protein" => false,
"multidomain_protein" => false,
"oligomeric_protein" => false,
"eukaryotic_protein" => false,
"protein_protein_complex" => false,
"protein_nucleic_acid_complex" => false,
"protein_ligand_complex" => false,
"de_novo_designed_protein" => false,
"post_translational_modification" => false
),
"ProteinClone" => array(
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array()
)
)
$filteredLabs = array(
"UVA",
"NU",
"UT",
"WU"
)
$highlighted = array()
$paths = array(
array(
"Target___006146"
),
array(
"Target___006146",
"ProteinClone___66385"
),
array(
"Target___006146",
"ProteinClone___76933"
),
array(
"Target___006146",
"ProteinClone___66386"
),
array(
"Target___006146",
"ProteinClone___73999"
),
array(
"Target___006146",
"ProteinClone___60789"
),
array(
"Target___006146",
"ProteinClone___60681"
),
array(
"Target___006146",
"ProteinClone___60585"
),
array(
"Target___006146",
"ProteinClone___76996"
),
array(
"Target___006146",
"ProteinClone___76996",
"Expression___33659"
),
array(
"Target___006146",
"ProteinClone___76996",
"Expression___58141"
)
)
$tips = array(
"Target___006146" => array(
"title" => "Target 006146",
"text" => "RecName: Full=Osteoclast-associated immunoglobulin-like receptor; Short=Osteoclast-associated receptor; Short=mOSCAR; AltName: Full=Ocl178; Flags: Precursor"
),
"ProteinClone___66385" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pSGC-His<br>person: Mark Stead"
),
"ProteinClone___76933" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pIEX-sec-C<br>person: Mark Stead"
),
"ProteinClone___66386" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pPELB30<br>person: Mark Stead"
),
"ProteinClone___73999" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pDAD-SEC<br>person: Mark Stead"
),
"ProteinClone___60789" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pIEX-sec-C<br>person: Brandan Hillerich"
),
"ProteinClone___60681" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pMAM-Fc<br>person: Brandan Hillerich"
),
"ProteinClone___60585" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pDAD-Fc<br>person: Brandan Hillerich"
),
"ProteinClone___76996" => array(
"title" => "Clone",
"text" => "sequence range: 31-125<br>vector: pIEX-sec-C<br>person: Mark Stead"
),
"Expression___33659" => array(
"title" => "Expression",
"text" => "expression level: 0.0%<br>solubility level: 0.0%<br>media: Express Five SFM (4mL)<br>induction: IPTG (37°C)<br>person: Albe Chan"
),
"Expression___58141" => array(
"title" => "Expression",
"text" => "expression level: 66.7%<br>solubility level: 66.7%<br>media: Express Five SFM (3000mL)<br>induction: IPTG (37°C)<br>person: Scott Garforth"
),
"Purification___5313" => array(
"title" => "Purification",
"text" => "final concentration: 0.7mg/mL<br>SeMet: native<br>affinity tag: na<br>person: John Attonito"
)
)
$root = array(
"id" => "Target___006146",
"name" => "T 006146",
"data" => array()
)
$clones = array(
array(
"id" => "ProteinClone___66385",
"name" => "C .08/01/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___76933",
"name" => "C .03/20/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___66386",
"name" => "C .08/01/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___73999",
"name" => "C .01/07/13",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___60789",
"name" => "C .04/18/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___60681",
"name" => "C .04/13/12",
"data" => array(),
"children" => array()
),
array(
"id" => "ProteinClone___60585",
"name" => "C .04/13/12",
"data" => array(),
"children" => array()
)
)
$sclone = array(
"id" => "76996",
"target_id" => "006146",
"clone_suffix" => "36599",
"sequence_start" => "31",
"sequence_end" => "125",
"sequence" => "QPWLGAHPAAVVTPGINVTLTCRAPQSAWRFALFKSGLVTPLLLRDVSVELAEFFLEEVTPAQGGSYHCRYRKTDWGPGVWSQPSNVLELLVTDQ",
"sequence_comments" => null,
"local_protein_target_id" => "10349",
"local_clone_plate_id" => null,
"local_clone_id" => "36599",
"experiment_date_start" => "2013-03-20",
"experiment_date_end" => "2013-03-20",
"staff_id" => "430",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Ligation Independent Cloning",
"status" => "success",
"vector" => "pIEX-sec-C",
"pcr_primer_forward" => "AGGATTATGGAGGCCAGCCATGGCTGGGAGCTC",
"pcr_primer_backward" => "GATTGGAAGTAGAGGTTCTCTGCCTGATCCGTTACCAGCAGTTCC",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-03-20 15:00:17.163742+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:07:29.252093+00",
"upd_user_id" => "1",
"secondary_shipped_to_lab_id" => null,
"secondary_shipped_date" => null,
"external_source" => false,
"mutation" => null,
"bei_available" => false,
"bei_number" => null,
"reference_sequence_variance" => null,
"confirmed_dna_sequence" => null,
"confirmed_protein_sequence" => null,
"present_in_lims" => false,
"template_dna_sequence" => "CAGCCATGGCTGGGAGCTCATCCTGCTGCAGTTGTGACTCCTGGGATCAACGTGACCTTGACTTGCCGCGCACCTCAATCTGCCTGGCGGTTTGCACTCTTCAAAAGTGGCCTTGTCACCCCTCTGCTCCTCCGGGATGTGTCCGTTGAGCTGGCTGAGTTCTTCCTGGAAGAAGTGACTCCGGCCCAAGGGGGCAGTTATCACTGCCGCTACCGCAAGACAGACTGGGGGCCAGGTGTCTGGTCTCAGCCCAGTAATGTTCTGGAACTGCTGGTAACGGATCAG",
"lims_date" => "2013-03-20",
"dummy" => false,
"type" => null,
"clone_annotation" => null,
"optimized_dna_sequence" => null,
"optimized" => false,
"truncated" => false,
"synthetic" => false,
"Staff" => array(
"id" => "430",
"first_name" => "Mark",
"last_name" => "Stead",
"email" => "mark.stead@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2012-02-28 22:00:05.514568+00",
"updated" => "2012-02-28 22:00:05.514568+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "430"
),
"Expression" => array(
array(),
array(),
array()
)
)
$iclone = array(
"id" => "ProteinClone___76996",
"name" => "C .03/20/13",
"data" => array(),
"children" => array(
array()
)
)
$sexpr = array(
"id" => "58141",
"target_id" => "006146",
"expression_suffix" => "52911",
"clone_id" => "76996",
"clone_suffix" => "36599",
"local_clone_id" => "36599",
"local_protein_target_id" => "10349",
"local_expression_id" => "52911",
"experiment_date_start" => "2013-09-17",
"experiment_date_end" => "2013-09-17",
"staff_id" => "355",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large scale insect expression- secreted",
"status" => "success",
"expression_organism" => "Insect",
"expression_strain" => "High Five",
"media_type" => "Express Five SFM",
"media_volume" => "3000",
"growth_temperature" => "37",
"induction_temperature" => "37",
"induction_reagent" => "IPTG",
"experiment_type" => "production",
"expression_level" => "66.6667",
"solubility_level" => "66.6667",
"inserted" => "2013-09-23 14:00:28.84863+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:26:41.167465+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-09-23",
"dummy" => false,
"Staff" => array(
"id" => "355",
"first_name" => "Scott",
"last_name" => "Garforth",
"email" => "scott.garforth@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2011-03-22 14:36:38.247355+00",
"updated" => "2011-03-22 14:36:38.247355+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "355"
),
"Purification" => array(
array()
)
)
$iexpr = array(
"id" => "Expression___58141",
"name" => "E .09/17/13",
"data" => array(),
"children" => array()
)
$expression_level = "66.7%"
$solubility_level = "66.7%"
$spur = array(
"id" => "5313",
"target_id" => "006146",
"purification_suffix" => "6486",
"expression_id" => "58141",
"local_expression_id" => "52911",
"local_protein_target_id" => "10349",
"local_purification_id" => "6486",
"experiment_date_start" => "2013-09-23",
"experiment_date_end" => "2013-09-24",
"staff_id" => "450145",
"other_people" => null,
"lab_id" => "AECOM",
"protocol_id" => "Large-Scale Automated Protein Purification",
"status" => "success",
"description" => null,
"affinity_tag_status" => "na",
"semet_status" => "native",
"covalent_modification" => null,
"final_buffer" => null,
"final_concentration" => "0.7",
"final_volume" => "22110",
"shipped_to_lab_id" => null,
"shipped_date" => null,
"inserted" => "2013-09-26 18:00:37.958962+00",
"ins_user_id" => null,
"update" => "2014-05-19 02:29:51.605933+00",
"upd_user_id" => "1",
"present_in_lims" => false,
"lims_date" => "2013-09-26",
"dummy" => false,
"yield" => null,
"Staff" => array(
"id" => "450145",
"first_name" => "John",
"last_name" => "Attonito",
"email" => "john.attonito@einstein.yu.edu",
"phone" => null,
"lab_id" => "AECOM",
"responsibility" => null,
"databases" => false,
"admin" => false,
"protein_production" => false,
"crystallography" => false,
"pi" => false,
"lab_contact" => false,
"inserted" => "2013-08-23 01:00:02.115165+00",
"updated" => "2013-08-23 01:00:02.115165+00",
"institution_id" => null,
"middle_initials" => null,
"active" => true,
"manager" => false,
"function" => null,
"real_id" => "450145"
),
"CrystallizationDrop" => array(
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array(),
array()
),
"Hsqc" => array()
)
$ipur = array(
"id" => "Purification___5313",
"name" => "P .09/23/13"
)
Unitrack_SpaceTreeController::create_JSON() - /var/www/unitrack/controllers/unitrack_space_tree_controller.php, line 205
Unitrack_SpaceTreeController::view() - /var/www/unitrack/controllers/unitrack_space_tree_controller.php, line 48
Dispatcher::_invoke() - CORE/cake/dispatcher.php, line 204
Dispatcher::dispatch() - CORE/cake/dispatcher.php, line 171
[main] - APP/webroot/index.php, line 83