http://bioportal.bioontology.org Updates to the NCBO BioPortal Repository en-ushttp://bioportal.bioontology.org/ontologies/49136Ontology Evidence codes version 2.03 was added to the repositorybioontology.org2012-08-31 13:15:05 -0700http://bioportal.bioontology.org/ontologies/49097Ontology Evidence codes version 2.03 was added to the repositorybioontology.org2012-08-24 13:48:20 -0700http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_f0939c3a-73af-4fc2-8d0c-d77ecdab7022Comment: "ECO:0000298 cleavage arrested development" is now defined as "A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked."bioontology.org2011-03-03 15:23:41 -0800http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_d3956243-981c-4027-afee-88acfb540d01Comment: The term "ECO:0000299 cytochalasin experiment result" now reads: "A type of cleavage arrested development that arises after treatment with cytochalasin."bioontology.org2011-03-03 15:21:34 -0800http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_6db6ebb0-95a7-4c40-8718-f7598c4bb7d5Comment: The name of ECO:0000240 has been changed to "anatomical perturbation" and the definition has been changed to "Experimental phenotypic evidence where a structural feature of an organism is disrupted."bioontology.org2011-03-03 15:19:15 -0800http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_b38af084-04b0-4861-a14d-0c3c6e08a832Comment: "ECO:0000310 nano-cap analysis of gene expression" is defined: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching."bioontology.org2011-03-03 15:11:56 -0800http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_6575b5b2-8ad2-41b0-853c-ae0925e6a657Comment: "ECO:0000309 cap analysis of gene expression" is defined as: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system."bioontology.org2011-03-03 15:10:31 -0800http://bioportal.bioontology.org/notes/virtual/1012?noteid=Note_d87fb5f8-8cb3-477c-8765-00653d9f9b4dComment: "ECO:0000243 tissue grafting" has been created. Definition: "A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure."bioontology.org2011-03-03 15:08:33 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesComment: In this type of experiment, the experimentalist disrupts a given anatomical structure and monitors the effect of this disruption on the developmental program. Therefore the anatomical perturbation should be seen as a statement of perturbation and not as an assessment.bioontology.org2011-02-04 04:22:46 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesComment: [Term] id: ECO:0000299 name: cytochalasin experiment result def: "A type of cleavage-arrested development that arises after treatment with cytochalasin." [ECO:MCC]
comment: Cytochalasin inhibits cytoplasmic divisioncytokinesis by blocking the formation of contractile microfilaments.
is_a: ECO:0000298 ! cleavage arrested development bioontology.org2011-02-04 04:17:56 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesComment: [Term] id: ECO:0000298 name: cleavage-arrested development def: "A type of experimental phenotypic evidence in the embryos of certain species, where development proceeds although cytokinesis is blocked." [ECO:MCC]
comment: In the embryos of some organisms, inhibition of cytokinesis does not block the cell cycle, nor the unfolding of the developmental program. This allows to freeze the embryo morphology, and to analyze the developmental fate of each cell present at the time of cleavage arrest.
is_a: ECO:0000059 ! experimental phenotypic evidence bioontology.org2011-02-04 04:16:25 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesReason for request: In the next version of ANISEED database (be careful, new url : http://www.aniseed.cnrs.fr/) we will represent this type of experiment.
comment tag for this term:
nanoCAGE captures the 5? ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5? full length cDNAs is extended upon hybridization of the riboguanosine-tailed template-switching oligonucleotides to these extra cytosines. In the semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template-switching, semisuppressive PCR and EcoP151 cleavage, 25-bp tags are ligated to barcode-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis.bioontology.org2011-02-04 04:06:26 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesReason for request: In the next version of ANISEED database (be careful, new url : http://www.aniseed.cnrs.fr/) we will represent this type of experiment. comment: The cDNA synthesis was carried out by using a 25-?g mRNA and first-strand cDNA primer (oligo dT12-18) with SuperScript II RT in the presence of trehalose and sorbitol. Subsequently, full-length cDNA was selected with biotinylated cap-trapper. Linkers are attached to the 5’ ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI adjacent to the 5’ ends.MmeI cleaves cDNAs at a sequence 20 and 18 nucleotide away (3’) from its recognition site, creating a two base overhang. After amplification, the sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.bioontology.org2011-02-04 04:04:01 -0800http://bioportal.bioontology.org/visualize/44406/?conceptid=ECO%3A0000000#notesReason for request: in ANISEED database (http://aniseed-ibdm.univ-mrs.fr/) we enter data resulting from tissue graft. Thus, we need this term to annotate these data.bioontology.org2010-12-01 04:21:53 -0800http://bioportal.bioontology.org/ontologies/1012/?p=notesReason for request: In ANISEED database (http://aniseed-ibdm.univ-mrs.fr/) we enter phenotype resulting from graft or ablation. Thus, we need this this kind of term to annotate these data.bioontology.org2010-12-01 04:15:04 -0800