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MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions

Carrine E. Blank, Hong Cui, Lisa R. Moore, Ramona L. Walls
2016 Journal of Biomedical Semantics  
MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium  ...  During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life,  ...  of taxonomic descriptions.  ... 
doi:10.1186/s13326-016-0060-6 pmid:27076900 pmcid:PMC4830071 fatcat:hb4pncif7rhmlcciev6plkibtq

Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade, Hong Cui
2016 BMC Bioinformatics  
Conclusion: MicroPIE is a promising new tool for the rapid and efficient extraction of phenotypic character information from prokaryotic taxonomic descriptions.  ...  The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the  ...  Acknowledgements The authors thank Gail Gasparich of Towson University for providing us the Mollicutes descriptions and her constructive suggestions on the design of the evaluation experiment.  ... 
doi:10.1186/s12859-016-1396-8 pmid:27955641 pmcid:PMC5153691 fatcat:37vpr6l2dvfwdjarljzyydizwe

Natural Language Processing and Unsupervised Learning: It's Significance on Biomedical Literature

Kanika Gupta, Ashok Kumar
2018 International Journal of Current Research and Review  
arising in the biomedical research and would also help in the development of new hypothesis.  ...  There is massive information hidden in the biomedical literature in the form of scientific publications, book chapters, conference reports, etc.  ...  Authors also acknowledge the immense help received from the scholars whose articles are cited and included in references of this manuscript.  ... 
doi:10.31782/ijcrr.2018.10143 fatcat:n56phwi4mfa4jkwgutik5r64ze

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Lucia Muggia, Claudio G. Ametrano, Katja Sterflinger, Donatella Tesei
2020 Life  
Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota  ...  These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly  ...  Melanin can be found in culture fluids in the form of granules, which confer the culture supernatant a dark-brown coloration [287] .  ... 
doi:10.3390/life10120356 pmid:33348904 pmcid:PMC7765829 fatcat:lmcs2k47avetlhteuwegrui4a4

Export Signals [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Subsequently, class and order characters determined morphological characters and size of body parts by acquiring new regulatory and metabolic systems.  ...  ▶virus Environmental Deviation: Quantitative characters are manifested in a phenotypic value, called P that can be partitioned into a genotypic value G and an environmental deviation, E, i.e., P = G +  ...  The members of the hnRNP family (~20 proteins) are involved in the transport of mRNA. ▶RRE, ▶nuclear pore, ▶nuclear localization sequence, ▶Gle1, ▶Mex67, ▶RNA export, ▶RNA transport,  ... 
doi:10.1007/978-1-4020-6754-9_5734 fatcat:6qstuftdi5dhnbuulcl4m6nfme

Ecology [chapter]

James C. Dunford, Louis A. Somma, David Serrano, C. Roxanne Rutledge, John L. Capinera, Guy Smagghe, Eli Shaaya, David G. Riley, John L. Capinera, Steve H. Dreistadt, Susanne D. Dyby, John B. Heppner (+24 others)
2008 Encyclopedia of Entomology  
Subsequently, class and order characters determined morphological characters and size of body parts by acquiring new regulatory and metabolic systems.  ...  ▶virus Environmental Deviation: Quantitative characters are manifested in a phenotypic value, called P that can be partitioned into a genotypic value G and an environmental deviation, E, i.e., P = G +  ...  The members of the hnRNP family (~20 proteins) are involved in the transport of mRNA. ▶RRE, ▶nuclear pore, ▶nuclear localization sequence, ▶Gle1, ▶Mex67, ▶RNA export, ▶RNA transport,  ... 
doi:10.1007/978-1-4020-6359-6_3494 fatcat:zdm7o5n7jngerpge54q4mmczme

Breeding Climate-Resilient Bananas [chapter]

Allan Brown, Sebastien C. Carpentier, Rony Swennen
2020 Genomic Designing of Climate-Smart Fruit Crops  
Acknowledgements This study has been supported by Grants Nº 19308/PI/14 and Nº 19879/GERM/15 of the Seneca Foundation of the Region of Murcia and the Apricot Breeding project Converse (1987) , Tzanetakis  ...  (2010) , Petrzik et al. (1998), Thompson and Jelkman (2003) , , Tzanetakis et al. (2007) , Yoshikawa et al. (1986) , Yoshikawa and Inouye (1988) , Ratti et al. (2006) Nematode Jones and Wood  ...  Ontology of the terms used in phenotyping experiments should also correspond to the ontology defined in the vitis section of cropontology (www.cropontology.org/ontology/VITIS/Vitis).  ... 
doi:10.1007/978-3-319-97946-5_4 fatcat:cqzcfw6fnfcjtbnsw2bchzkx3q

Molecular Biology

2003 Revista do Instituto de Medicina Tropical de São Paulo  
The responsible CD36 binding domains are highly conserved in their three-dimensional structure, and can be used as components of an anti-adherent vaccine.  ...  Plasmodium vivax, the parasite responsible for about 80% of Brazilian malaria cases, and which causes great socio-economical burden for this region cannot be cultured continuously in vitro precluding the  ...  Alicia Kompalic-Cristo is a CONICIT and UCLA fellow.  ... 
doi:10.1590/s0036-46652003000700010 fatcat:e465qym5erbzng67al3i3rqww4

Abstracts from the 5th International Research Conference on Huanglongbing

Organization IOCV
2017 Journal of citrus pathology  
They were formatted but not edited by the Journal of Citrus Pathology. Recommended format for citing abstracts, using the first abstract below as an example, is as follows:  ...  Lcr falls in the latter category and is also the only member of this group that has successfully been cultured in artificial media.  ...  Other genes found in Lcr but not found in Las and that should significantly limit Las culturability are: glyoxylase I and the ATP/ADP translocase.  ... 
doi:10.5070/c441034714 fatcat:ytjrcafo7zh25ap2ij2uy7zbeu

Abstracts of Presentations at the 2016 APS Annual Meeting

2016 Phytopathology  
Naming and description of a number of other new fungal taxa are in progress.  ...  So biology control of tobacco disease attracts more and more attention. The usage of micro-organisms or microbial metabolites is an important approach in controlling nematodes.  ...  A comparison of culture media and temperature conditions demonstrated that four day old cultures of M. vaccinii-corymbosi isolate RL1 (Mvc-RL1) grown on oatmeal agar medium, in the dark, at 22°C followed  ... 
doi:10.1094/phyto-106-12-s4.1 pmid:27922801 fatcat:vztse3dj7rhkdkcokeku2sbqrq

Gout [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
A description of the procedure can be found: Brailo LH et al 1999 Mutation Res Genomics 406:45.  ...  Gellan Gum: A synthetic polysaccharide, used for solidifying plant tissue and bacterial culture media (instead of agar).  ...  Its homologs are present in prokaryotes as well as in the mitochondria of yeast, insects, and mammals.  ... 
doi:10.1007/978-1-4020-6754-9_7078 fatcat:igkfa5bydfeehhe7ekrw5dudny

Gramene (rice and other grasses database) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
A description of the procedure can be found: Brailo LH et al 1999 Mutation Res Genomics 406:45.  ...  Gellan Gum: A synthetic polysaccharide, used for solidifying plant tissue and bacterial culture media (instead of agar).  ...  Its homologs are present in prokaryotes as well as in the mitochondria of yeast, insects, and mammals.  ... 
doi:10.1007/978-1-4020-6754-9_7111 fatcat:dsqojxeco5gwhgpgdcm22jb33y

Mitochondrial Import [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Such assays can be done in cultured cells but in vivo assay of meiotic plant cells or mammalian bone marrow polychromatic erythrocytes have also been used.  ...  Single hybridoma cells are then cultured in multi-well culture vessels and screened for the production of specific MAbs by the use of radioimmunoassays (RIA) or by enzyme-linked immunosorbent assay (ELISA  ...  As an example, the mutagenicity in the Ames Salmonella assay of a few compounds is listed in the table.  ... 
doi:10.1007/978-1-4020-6754-9_10535 fatcat:kablmiledvdx3lxxk4j3tsicca

MITE (mariner insect transposon-like element, miniature inverted-repeat transposable element) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Such assays can be done in cultured cells but in vivo assay of meiotic plant cells or mammalian bone marrow polychromatic erythrocytes have also been used.  ...  Single hybridoma cells are then cultured in multi-well culture vessels and screened for the production of specific MAbs by the use of radioimmunoassays (RIA) or by enzyme-linked immunosorbent assay (ELISA  ...  As an example, the mutagenicity in the Ames Salmonella assay of a few compounds is listed in the table.  ... 
doi:10.1007/978-1-4020-6754-9_10520 fatcat:tj67vdv34vc63hlfupk6xahu24

SPECIAL ISSUE: ABSTRACTS FROM THE 2008 ISSOL MEETING

2009 Origins of life and evolution of the biosphere  
Optical and x-ray emission spectroscopy of high-power laser-induced dielectric breakdown in molecular gases and their mixtures. Journal of Physical Chemistry A, 110:12113-12120.  ...  Acknowledgements This work financially supported by Grant Agency of the Czech Republic (grant No. 203/06/ 1278) and the Czech Ministry of Education (grants LC510, LC528, and LA08024).  ...  Some of these cultures were added to a sterile Mars soil simulant, JSC Mars-1, some were kept in their sealed anaerobic culture tubes in liquid media, and some were centrifuged followed by removal of the  ... 
doi:10.1007/s11084-009-9164-7 pmid:19468860 pmcid:PMC2691805 fatcat:zv2le4yeirbrtowyyqc3m5lcom
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