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GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong, Robert D. Finn
2016 Database: The Journal of Biological Databases and Curation  
Citation details: Sangrador-Vegas,A., Mitchell,A., Chang,H.-Y. et al. GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. Abstract The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation. As a corollary, annotation stability is considered to be a measure of reliability. However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and
more » ... he protein family databases that are built upon the sequence databases and used to help annotate them. Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator.
doi:10.1093/database/baw027 pmid:26994912 pmcid:PMC4799721 fatcat:lwve4cepezbcvi6t2k6odynq4u

Agreement on Nucleic Acid Manual versus Automated Extraction Methods and Commercial Available Polymerase Chain Reaction (PCR) Assays for SARS-CoV-2

Su Kelvin Sieng-Bing, Lee Jeffrey Soon-Yit, Yong Sook-Min, Kamilah Binti Dahian, Wong Chew-Ee, Nur Alfreena Binti Alfie, Ting Siew-Ming, Toh Teck-Hock
2021 Zenodo  
The availability of multiple PCR assays and extraction methods for SARS-CoV-2 viral ribonucleic acid cause a concern on their agreement. Validation tests have been conducted when new assays or extraction methods are introduced to understand their performance. This study evaluates the agreement of the results between different extraction methods and PCR assays. Methods: We searched the laboratory data in Sibu Hospital Clinical Research Centre Laboratory for any PCR validation results from 1
more » ... ry to 31 May 2021 using two or more assays or extraction methods. A pooled gold standard was created by defining any samples detected positive using any extraction methods or assays. Wecalculatedtheaccuracyparameters. We compared the cyclic threshold (Ct) value for positivegenesinbothPCRassays. Results: The agreements for samples extracted manually versus automated method and run on Seegene was 0.869; on BioSewoom was 0.899. When extracted manually or using automated, the agreements for two different assays were 0.911 and 1.000, respectively. Cyclic threshold (Ct) using automated extraction was significantly lower in both assays (p<0.001). Compared to the pooled gold standard, both assays performed well using automated extraction, but BioSewoom extracted manually had lower sensitivity (86.67%; 95% CI: 69.28, 96.24) and negative predictive value (96.49%; 95% CI: 91.70, 98.56). Conclusion: The assays and extraction methods were generally in good agreement and accurate, albeit some differences. It is important to understand their performance to guide the interpretation and assist in patients management and pandemic. [Disclaimer: Abstract text might vary slightly from what is displayed in the e-poster]
doi:10.5281/zenodo.5461111 fatcat:z4qwej36lrfurmxbea57z5m7ta

Interaction of Dietary Linoleic Acid and α-Linolenic Acids with rs174547 in FADS1 Gene on Metabolic Syndrome Components among Vegetarians

Yuan Kei Ching, Yit Siew Chin, Mahenderan Appukutty, Vasudevan Ramanchadran, Choo Yee Yu, Geik Yong Ang, Wan Ying Gan, Yoke Mun Chan, Lay Kek Teh, Mohd Zaki Salleh
2019 Nutrients  
Fatty acid desaturase 1 (FADS1) gene controls the fatty acid metabolism pathway in the human body. The lower intake of α-linolenic acid (ALA) than linoleic acid (LA) among vegetarians may disrupt the fatty acid metabolism and limit the conversion of ALA to anti-inflammatory products such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). This cross-sectional study aimed to determine the interaction of rs174547 in FADS1 gene with LA and ALA on metabolic syndrome (MetS) components. A
more » ... otal of 200 Chinese and Indian vegetarians in Kuala Lumpur and Selangor, Malaysia participated in the present study. The data on socio-demographic characteristics, vegetarianism practices, dietary practices, anthropometric measurements, blood pressure (BP), and overnight venous fasting blood samples were collected from the vegetarians. The rs174547 in FADS1 gene was significantly associated with MetS and its components such as waist circumference (WC) and fasting blood glucose (FBG). Multiple logistic regression analyses revealed that vegetarians with TT genotype of rs174547 in FADS1 gene had higher odds for MetS, larger WC, higher BP, and a lower level of HDL-c. Two-way ANOVA analysis showed that LA interacts with rs174547 in FADS1 gene to affect HDL-c (p < 0.05) among vegetarians. The present findings suggest the need to develop dietary guidelines for vegetarians in Malaysia. Prospective studies are also needed to affirm the interaction between LA and rs174547 in FADS1 gene on HDL-c among Malaysian vegetarians.
doi:10.3390/nu11071686 fatcat:vmsnlooamrg4hozsagpvhsqrjy

The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
The InterPro database ( interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures,
more » ... apitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro Figure 1. InterPro matches for UniProtKB entry Q3JCG5 showing predicted protein family membership, domains and sites.
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Alex L Mitchell, Teresa K Attwood, Patricia C Babbitt, Matthias Blum, Peer Bork, Alan Bridge, Shoshana D Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew I Fraser, Julian Gough, David R Haft (+30 others)
2018 Nucleic Acids Research  
doi:10.1093/nar/gky1100 pmid:30398656 fatcat:ccbjkaabarhazk3yclk2vjjqoq

Vitamin D deficiency during pregnancy and its associated factors among third trimester Malaysian pregnant women

Fui Chee Woon, Yit Siew Chin, Intan Hakimah Ismail, Marijka Batterham, Amir Hamzah Abdul Latiff, Wan Ying Gan, Geeta Appannah, Siti Huzaifah Mohammed Hussien, Muliana Edi, Meng Lee Tan, Yoke Mun Chan, Samson Gebremedhin Gebreselassie
2019 PLoS ONE  
Similarly, a recent local study conducted by Yong et al. [36] demonstrated that milk and dairy products were the major food sources contributing to vitamin D intake among pregnant women.  ...  Supervision: Yit Siew Chin. Writing -original draft: Fui Chee Woon.  ...  Formal analysis: Fui Chee Woon, Yit Siew Chin, Marijka Batterham, Siti Huzaifah Mohammed Hussien, Muliana Edi, Meng Lee Tan. Funding acquisition: Fui Chee Woon, Yit Siew Chin.  ... 
doi:10.1371/journal.pone.0216439 pmid:31233513 pmcid:PMC6590777 fatcat:kvoc7m5jxzgg3nzk3sv3inj3om

Page 2041 of American Society of Civil Engineers. Collected Journals Vol. 119, Issue Index [page]

American Society of Civil Engineers. Collected Journals  
Drainage Efficiency of Sand Layer in Layered Clay-Sand Reclamation, Siew-Ann Tan, Kee- Ming oe Kwet-Yew Yong and Seng-Lip Lee, GT Feb. 92, p209-228.  ...  Ultimate Settlement by Hyperbolic Plot for Clays with Vertical Drains, Siew-Ann Tan, GT May 93, p950-956. Undrained Strength Interrelationships Among CIUC, UU, and UC Tests, Yit-Jin Chen and Fred H.  ... 

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

Rachael P Huntley, Tony Sawford, Maria J Martin, Claire O'Donovan
2014 GigaScience  
Acknowledgements We would like to thank the GO Consortium, the UniProt Consortium and from InterPro: Alex Mitchell, Amaia Sangrador, Hsin-Yu Chang and Siew-Yit Yong.  ... 
doi:10.1186/2047-217x-3-4 pmid:24641996 pmcid:PMC3995153 fatcat:knk77iflwfhajog645c3kxgmcu

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
2020 Nucleic Acids Research  
Yong.  ...  ACKNOWLEDGEMENTS The authors would like to thank former members of the InterPro team: Sara El-Gebali, Matthew Fraser, Aurélien Luciani, Sebastien Pesseat, Simon Potter, Neil Rawlings, Amaia Sangrador-Vegas and Siew-Yit  ... 
doi:10.1093/nar/gkaa977 pmid:33156333 pmcid:PMC7778928 fatcat:vfs7k3dxr5bcpbpvxbptj6r46m

The Development of the Malayan Chinese Association

Heng Pek Koon
Kin Kwok Yit Pau. 28 April 1955. 2.  ...  ., Pickering Protector of Chinese, and Ng Siew Yong, "The Chinese Protectorate in Singapore 1877-1900", JSEAH, Vol.2, no.l, March 1961.  ... 
doi:10.25501/soas.00033754 fatcat:6osiexpvqbh3pbrskwykmayum4

Chinese education in Malaya : one dimension of the problems of Malayan motherhood

William Chang Nang Hsu
Tan Siew Sin noted in 1961 that Chinese parents were voluntarily sending their children to schools using English as the medium of instruction.  ...  Tan Siew Sin explained that the "clear ultimate object of the two bodies [the UCSTA and the UCSMC3 was recognition of Chinese as the official language.  ... 
doi:10.14288/1.0103998 fatcat:fdnkjvtdifeojaibve4mjqbqb4

On Fitting Finite Dirichlet Mixture Using ECM and MML [chapter]

Nizar Bouguila, Djemel Ziou
2005 Lecture Notes in Computer Science  
,YiT), in which random variable Yit = 1 at decision maker i response variables t choosing alternative 1 and Yit =0 at decision maker i response variables t choosing alternative 0.  ...  Yit is tnd response variables from decision maker i and value Yit is binary. Response of decision maker i can be expressed as Yi = (Yi1,....  ... 
doi:10.1007/11551188_19 fatcat:gtzi5u6emvfyxea3zbklobnvom

Economic plans and the evolution of economic nationalism in Siam in the 1930s

Makoto Nanbara
Poh, 5,000, Wah Sen Yit Poh, 6,000-7,000, Wah Khiew Yit P o h , 5 ,00 0-6 ,00 0, Hwa Siew Yer Pao, 1,000, Min Kok Yit Poh, 4 ,00 0-5 ,00 0, Bangkok Morning News, 4,000-5,000. 50 Constance M.  ...  Bangkok: Aksornsan, 1988, p.338. 92 Ibid., pp.343-4. 90 Chalermkiat Phiunaun, Botkwam prakopkan sammana kung satawat Thammasat: 2 4 7 7 -2 5 2 7 ruang khwam khit thang kanm uang khong Pridi Phanom yong  ... 
doi:10.25501/soas.00028468 fatcat:zsyvw72yvvhohdg64wfauqcswm

News flows in Singapore

Carl Alexander Haentzschel, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
The Chong Shing Yit Pao was established in 1907 and closed down two years later. And the Sun Pao was introduced in 1909 and shut down just a few months after.  ...  added a comment in which he repeated that Edgar D'Souza was the main source of the article. 773 the meantime, James Fu had sent another letter to the editor which was also published in Archibishop Yong  ... 
doi:10.18452/15736 fatcat:3anppd2vtzbcnmuuo7dbaltepa