Volume 2017; Issue 1

Main
Database
Volume 2017; Issue 1

Database

Volume 2017; Issue 1

1

Biocuration in the structure–function linkage database: the anatomy of a superfamily

Holliday, Gemma L., Brown, Shoshana D., Akiva, Eyal, Mischel, David, Hicks, Michael A., Morris, John H., Huang, Conrad C., Meng, Elaine C., Pegg, Scott C.-H., Ferrin, Thomas E., Babbitt, Patricia C.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

2

Strategies towards digital and semi-automated curation in RegulonDB

Rinaldi, Fabio, Lithgow, Oscar, Gama-Castro, Socorro, Solano, Hilda, López-Fuentes, Alejandra, Muñiz Rascado, Luis José, Ishida-Gutiérrez, Cecilia, Méndez-Cruz, Carlos-Francisco, Collado-Vides, Julio

Journal:

Year:

2017

Language:

english

File:

PDF, 1.88 MB

english, 2017

3

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

Suhrbier, L., Kusber, W.-H., Tschöpe, O., Güntsch, A., Berendsohn, W. G.

Journal:

Year:

2017

Language:

english

File:

PDF, 10.61 MB

english, 2017

4

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis

Balderas-Martínez, Yalbi Itzel, Rinaldi, Fabio, Contreras, Gabriela, Solano-Lira, Hilda, Sánchez-Pérez, Mishael, Collado-Vides, Julio, Selman, Moisés, Pardo, Annie

Journal:

Year:

2017

Language:

english

File:

PDF, 904 KB

english, 2017

5

Exploring convolutional neural networks for drug–drug interaction extraction

Suárez-Paniagua, Víctor, Segura-Bedmar, Isabel, Martínez, Paloma

Journal:

Year:

2017

Language:

english

File:

PDF, 885 KB

english, 2017

6

miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways

Subhra Das, Sankha, James, Mithun, Paul, Sandip, Chakravorty, Nishant

Journal:

Year:

2017

Language:

english

File:

PDF, 1.17 MB

english, 2017

7

TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer

Postic, Guillaume, Ghouzam, Yassine, Etchebest, Catherine, Gelly, Jean-Christophe

Journal:

Year:

2017

Language:

english

File:

PDF, 528 KB

english, 2017

8

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

Jiang, Xiangying, Ringwald, Martin, Blake, Judith, Shatkay, Hagit

Journal:

Year:

2017

Language:

english

File:

PDF, 410 KB

english, 2017

9

Carotenoids Database: structures, chemical fingerprints and distribution among organisms

Yabuzaki, Junko

Journal:

Year:

2017

Language:

english

File:

PDF, 912 KB

english, 2017

10

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases

Xu, Yanjun, Yang, Haixiu, Wu, Tan, Dong, Qun, Sun, Zeguo, Shang, Desi, Li, Feng, Xu, Yingqi, Su, Fei, Liu, Siyao, Zhang, Yunpeng, Li, Xia

Journal:

Year:

2017

Language:

english

File:

PDF, 903 KB

english, 2017

11

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Ruas, Max, Guignon, V., Sempere, G., Sardos, J., Hueber, Y., Duvergey, H., Andrieu, A., Chase, R., Jenny, C., Hazekamp, T., Irish, B., Jelali, K., Adeka, J., Ayala-Silva, T., Chao, C.P., Daniells, J.,

Journal:

Year:

2017

Language:

english

File:

PDF, 1.88 MB

english, 2017

12

BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences

Ravikumar, K.E., Rastegar-Mojarad, Majid, Liu, Hongfang

Journal:

Year:

2017

Language:

english

File:

PDF, 1.12 MB

english, 2017

13

VerSeDa: vertebrate secretome database

Cortazar, Ana R., Oguiza, José A., Aransay, Ana M., Lavín, José L.

Journal:

Year:

2017

Language:

english

File:

PDF, 456 KB

english, 2017

14

Outreach and online training services at the Saccharomyces Genome Database

MacPherson, Kevin A., Starr, Barry, Wong, Edith D., Dalusag, Kyla S., Hellerstedt, Sage T., Lang, Olivia W., Nash, Robert S., Skrzypek, Marek S., Engel, Stacia R., Cherry, J. Michael

Journal:

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

15

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

Güntsch, Anton, Hyam, Roger, Hagedorn, Gregor, Chagnoux, Simon, Röpert, Dominik, Casino, Ana, Droege, Gabi, Glöckler, Falko, Gödderz, Karsten, Groom, Quentin, Hoffmann, Jana, Holleman, Ayco, Kempa, Ma

Journal:

Year:

2017

Language:

english

File:

PDF, 1.21 MB

english, 2017

16

The HIV oligonucleotide database (HIVoligoDB)

Carneiro, João, Resende, Adriana, Pereira, Filipe

Journal:

Year:

2017

Language:

english

File:

PDF, 477 KB

english, 2017

17

RAIN: RNA–protein Association and Interaction Networks

Journal:

Year:

2017

File:

PDF, 176 KB

2017

18

Workflow and web application for annotating NCBI BioProject transcriptome data

Vera Alvarez, Roberto, Medeiros Vidal, Newton, Garzón-Martínez, Gina A., Barrero, Luz S., Landsman, David, Mariño-Ramírez, Leonardo

Journal:

Year:

2017

Language:

english

File:

PDF, 1.46 MB

english, 2017

19

HopBase: a unified resource for Humulus genomics

Hill, Steven T., Sudarsanam, Ramcharan, Henning, John, Hendrix, David

Journal:

Year:

2017

Language:

english

File:

PDF, 946 KB

english, 2017

20

The ‘straight mouse’: defining anatomical axes in 3D embryo models

Armit, Chris, Hill, Bill, Venkataraman, S., McLeod, Kenneth, Burger, Albert, Baldock, Richard

Journal:

Year:

2017

Language:

english

File:

PDF, 776 KB

english, 2017

21

Curated protein information in the Saccharomyces genome database

Hellerstedt, Sage T., Nash, Robert S., Weng, Shuai, Paskov, Kelley M., Wong, Edith D., Karra, Kalpana, Engel, Stacia R., Cherry, J. Michael

Journal:

Year:

2017

Language:

english

File:

PDF, 891 KB

english, 2017

22

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)

Xu, Zhenzhen, Liu, Jing, Ni, Wanchao, Peng, Zhen, Guo, Yue, Ye, Wuwei, Huang, Fang, Zhang, Xianggui, Xu, Peng, Guo, Qi, Shen, Xinlian, Du, Jianchang

Journal:

Year:

2017

Language:

english

File:

PDF, 1.37 MB

english, 2017

23

Better living through ontologies at the Immune Epitope Database

Vita, Randi, Overton, James A., Sette, Alessandro, Peters, Bjoern

Journal:

Year:

2017

Language:

english

File:

PDF, 672 KB

english, 2017

24

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

McIlroy, Simon Jon, Kirkegaard, Rasmus Hansen, McIlroy, Bianca, Nierychlo, Marta, Kristensen, Jannie Munk, Karst, Søren Michael, Albertsen, Mads, Nielsen, Per Halkjær

Journal:

Year:

2017

Language:

english

File:

PDF, 1.53 MB

english, 2017

25

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Ruffier, Magali, Kähäri, Andreas, Komorowska, Monika, Keenan, Stephen, Laird, Matthew, Longden, Ian, Proctor, Glenn, Searle, Steve, Staines, Daniel, Taylor, Kieron, Vullo, Alessandro, Yates, Andrew, Z

Journal:

Year:

2017

Language:

english

File:

PDF, 1014 KB

english, 2017

26

Literature consistency of bioinformatics sequence databases is effective for assessing record quality

Bouadjenek, Mohamed Reda, Verspoor, Karin, Zobel, Justin

Journal:

Year:

2017

Language:

english

File:

PDF, 2.32 MB

english, 2017

27

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

Tordai, Hedvig, Jakab, Kristóf, Gyimesi, Gergely, András, Kinga, Brózik, Anna, Sarkadi, Balázs, Hegedűs, Tamás

Journal:

Year:

2017

Language:

english

File:

PDF, 494 KB

english, 2017

28

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

Putman, Tim E., Lelong, Sebastien, Burgstaller-Muehlbacher, Sebastian, Waagmeester, Andra, Diesh, Colin, Dunn, Nathan, Munoz-Torres, Monica, Stupp, Gregory S., Wu, Chunlei, Su, Andrew I., Good, Benjam

Journal:

Year:

2017

Language:

english

File:

PDF, 986 KB

english, 2017

29

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

Dorel, Mathurin, Viara, Eric, Barillot, Emmanuel, Zinovyev, Andrei, Kuperstein, Inna

Journal:

Year:

2017

Language:

english

File:

PDF, 1.68 MB

english, 2017

30

Automated PDF highlighting to support faster curation of literature for Parkinson’s and Alzheimer’s disease

Wu, Honghan, Oellrich, Anika, Girges, Christine, de Bono, Bernard, Hubbard, Tim J.P., Dobson, Richard J.B.

Journal:

Year:

2017

Language:

english

File:

PDF, 978 KB

english, 2017

31

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

Fishilevich, Simon, Nudel, Ron, Rappaport, Noa, Hadar, Rotem, Plaschkes, Inbar, Iny Stein, Tsippi, Rosen, Naomi, Kohn, Asher, Twik, Michal, Safran, Marilyn, Lancet, Doron, Cohen, Dana

Journal:

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

32

Strategies towards digital and semi-automated curation in RegulonDB

Rinaldi, Fabio, Lithgow, Oscar, Gama-Castro, Socorro, Solano, Hilda, López-Fuentes, Alejandra, Muñiz Rascado, Luis José, Ishida-Gutiérrez, Cecilia, Méndez-Cruz, Carlos-Francisco, Collado-Vides, Julio

Journal:

Year:

2017

Language:

english

File:

PDF, 183 KB

english, 2017

33

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

Sen, Taner Z., Braun, Bremen L., Schott, David A., Portwood, II, John L., Schaeffer, Mary L., Harper, Lisa C., Gardiner, Jack M., Cannon, Ethalinda K., Andorf, Carson M.

Journal:

Year:

2017

Language:

english

File:

PDF, 370 KB

english, 2017

34

TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species

Márcia de Oliveira, Luciana, Nogueira de Brito, Raissa, Anderson Souza Guimarães, Paul, Vitor Mastrângelo Amaro dos Santos, Rômulo, Gonçalves Diotaiuti, Liléia, de Cássia Moreira de Souza, Rita, Conce

Journal:

Year:

2017

Language:

english

File:

PDF, 709 KB

english, 2017

35

CHOmine: an integrated data warehouse for CHO systems biology and modeling

Gerstl, Matthias P., Hanscho, Michael, Ruckerbauer, David E., Zanghellini, Jürgen, Borth, Nicole

Journal:

Year:

2017

Language:

english

File:

PDF, 325 KB

english, 2017

36

In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis

Franco, Matheus Eloy, Bitencourt, Tamires Aparecida, Marins, Mozart, Fachin, Ana Lúcia

Journal:

Year:

2017

Language:

english

File:

PDF, 769 KB

english, 2017

37

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

Suhrbier, L., Kusber, W.-H., Tschöpe, O., Güntsch, A., Berendsohn, W. G.

Journal:

Year:

2017

Language:

english

File:

PDF, 183 KB

english, 2017

38

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species

Challis, Richard J., Kumar, Sujai, Stevens, Lewis, Blaxter, Mark

Journal:

Year:

2017

Language:

english

File:

PDF, 364 KB

english, 2017

39

Triage by ranking to support the curation of protein interactions

Mottin, Luc, Pasche, Emilie, Gobeill, Julien, Rech de Laval, Valentine, Gleizes, Anne, Michel, Pierre-André, Bairoch, Amos, Gaudet, Pascale, Ruch, Patrick

Journal:

Year:

2017

Language:

english

File:

PDF, 830 KB

english, 2017

40

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species

Malhotra, Sony, Mugumbate, Grace, Blundell, Tom L., Higueruelo, Alicia P.

Journal:

Year:

2017

Language:

english

File:

PDF, 556 KB

english, 2017

41

decodeRNA— predicting non-coding RNA functions using guilt-by-association

Lefever, Steve, Anckaert, Jasper, Volders, Pieter-Jan, Luypaert, Manuel, Vandesompele, Jo, Mestdagh, Pieter

Journal:

Year:

2017

Language:

english

File:

PDF, 810 KB

english, 2017

42

Text mining and expert curation to develop a database on psychiatric diseases and their genes

Gutiérrez-Sacristán, Alba, Bravo, Àlex, Portero-Tresserra, Marta, Valverde, Olga, Armario, Antonio, Blanco-Gandía, M.C., Farré, Adriana, Fernández-Ibarrondo, Lierni, Fonseca, Francina, Giraldo, Jesús,

Journal:

Year:

2017

Language:

english

File:

PDF, 716 KB

english, 2017

43

NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy

Ni, Yueqiong, Jensen, Kasper, Kouskoumvekaki, Irene, Panagiotou, Gianni

Journal:

Year:

2017

Language:

english

File:

PDF, 705 KB

english, 2017

44

Biocuration in the structure–function linkage database: the anatomy of a superfamily

Holliday, Gemma L., Brown, Shoshana D., Akiva, Eyal, Mischel, David, Hicks, Michael A., Morris, John H., Huang, Conrad C., Meng, Elaine C., Pegg, Scott C.-H., Ferrin, Thomas E., Babbitt, Patricia C.

Journal:

Year:

2017

Language:

english

File:

PDF, 177 KB

english, 2017

45

LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis

Torres, Felipe, Arias-Carrasco, Raúl, Caris-Maldonado, José C., Barral, Aldina, Maracaja-Coutinho, Vinicius, De Queiroz, Artur T. L.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.08 MB

english, 2017

46

PigVar: a database of pig variations and positive selection signatures

Zhou, Zhong-Yin, Li, Aimin, Otecko, Newton O., Liu, Yan-Hu, Irwin, David M., Wang, Lu, Adeola, Adeniyi C., Zhang, Junying, Xie, Hai-Bing, Zhang, Ya-Ping

Journal:

Year:

2017

Language:

english

File:

PDF, 1.58 MB

english, 2017

47

MGFD: the maize gene families database

Sheng, Lei, Jiang, Haiyang, Yan, Hanwei, Li, Xiaoyu, Lin, Yongxiang, Ye, Hui, Cheng, Beijiu

Journal:

Year:

2017

File:

PDF, 174 KB

2017

48

Chemical-induced disease relation extraction via convolutional neural network

Gu, Jinghang, Sun, Fuqing, Qian, Longhua, Zhou, Guodong

Journal:

Year:

2017

Language:

english

File:

PDF, 594 KB

english, 2017

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