Questions related to Database Searching
If we do not have anybody to do quality assurance (QA) of a large number of papers that we get from database searches, say, for example, about a 1000 papers, for a review paper, then what should one do?
The PRISMA guideline mentions that a second person should review the papers that are included into a review paper (scoping or systematic, etc), but if we do not have anybody to review this large number of papers (for example, 1000 papers) for eligibility, then what should be done? Please help.
I am looking to recover all proteins that are shared (e.g., to sequence similarity of 50%) between two species (e.g., Nicotiana tabacum and Arabidopsis thaliana). Is there a way to use UniProt's search tool to do this systematically? Alternatively, are there any better databases for this?
Thanks in advance for any advice!
One question related to science database search. I want to search SCI database to verify if paper is indexed or not. I searched through web of science, and as result I get one of my paper but does this mean that it s indexed in SCI database? thx, any comments are welcome.
Whenever researchers start with evidence-based reviews, whether they are scoping, rapid reviews, systematic reviews, or even current form of narrative reviews, they face problems at every steps which require assistance from people who have already been doing these kind of reviews. These problems can range from topic selection, to team formation to database search to registration and many more. Here I would like to initiate a discussion to identify the problems
faced by each and every researcher who is either planning to start or is currently doing reviews and welcome views to look for solutions for these problems with a collective approach.
The Mercator Institute for Literacy and Language Education at the University of Cologne, Germany, is conducting a systematic review on the effectiveness of language integrated strategies (e.g. scaffolding, Sheltered Instruction Observation Protocol (SIOP)) in classrooms. In this review, it is intended to collate, critically appraise and synthesize existing research evidence according to pre-defined criteria.
To complement our electronic database search, we are looking for manuscripts/working papers/project reports/dissertations (except for BA-/MA-thesis) that have not (yet) been published or submitted for publication (and are not (yet) indexed in databases).
We are interested in (quasi-)experimental and observational studies using a control group design that (statistically) examine
- the effectiveness of concepts of instruction that integrate language support and subject teaching
- for children of primary or secondary school age.
If you have carried out this type of study or if first results of an ongoing study are available, we would like to kindly request the document. Submitted studies will be reviewed by the project team; studies that match the review inclusion criteria will be included in the final review synthesis (i.e. summarized and discussed). Publication of the results is planned for 2021.
Of course, your submissions will only be used within the scope of the review and will not be passed to third parties.
Please send documents by September 30th, 2019 to Leonie Twente at email@example.com. If you have any questions, please contact Till Woerfel at firstname.lastname@example.org. Alternatively you can use the comment field below.
Thank you for your support!
Till Woerfel, Martha Höfler, Annika Witte, Anastasia Knaus, Rebekka Wanka and Leonie Twente
Further information about our systematic review can be found on our website: https://www.mercator-institut-sprachfoerderung.de/en/research-development/current-projects/systematic-narrative-review/
I'm conducting a systematic literature review about people's pro-environmental behaviour. I'm using Scopus and Google Scholar as my academic databases for searching peer-reviewed articles. Wondering if the two databases are enough or I should add other databases as well? Interestingly, I noticed that most of the papers I found in Web of Science are already included in Scopus too but not vice versa. Any advice or comments appreciated.
Dear Colleagues, We are currently conducting a meta-analysis on sex-specific genetic variances of fitness components. Specifically, we aim to test whether additive genetic variances of reproductive success (and other fitness correlates) differ between males and females. Because meta-analyses are often sensitive to publication bias, we are looking for unpublished datasets that quantified genetic variances of both sexes within the same experimental setup or field population. Ideally, the data should include sample size, mean estimate, unstandardized genetic variance, coefficient of variation, and heritability estimates for both sexes. If you have, or know of, such unpublished data sets, we would love to hear about it. Moreover, we would be very grateful if you could point us to published work that provides this type of information but may go unnoticed in database searches applying search terms like ‘genetic variation’, ‘heritability’ and ‘reproductive success’. Please email suggestions or questions to: email@example.com Many, many thanks in advance! Tim Janicke (CEFE-CNRS, Montpellier) with Lennart Winkler (Technische Universitaet Dresden) Maria Moiron (CEFE-CNRS, Montpellier) Ted Morrow (University of Sussex)
I have several pathways and want to know the biological process and metabolism related to each pathway.
Is there any database to search them?
For example I want to know the DRUG METABOLISM CYTOCHROME P450 pathway involved in what biological mechanisms or process?
I have undertaken a database search and identified the articles. I would like to evaluate the effectiveness of this search. Does the number of included studied identified by both databases count?
I'm interested in identifying proteins from egg whites through LC-MS and MALDI-TOF, then through database searching. The protocol that I was reading requires dialysis. Can I opt for centrifugation instead?
Please suggestions about finding numbers (statistics, figures) about a certain topic that you have in mind but not if the numbers are available. For example, number of hours people spend deliberating about which career to choose vs the number of hours doing that career. Or number of hours people spend deliberating about which career to choose vs number of hours doing they deliberate for much much less important decisions like what clothes they should buy?How do I find numbers related to career deliberation? Both tips about the general "number finding" issue and the specific "career deliberation" issue are appreciated .
Can anyone with CSD access help me with a following cell parameter if any structure exists:
a=11.18Å, α=81.97°, V=2191 Å,
b=12.63 Å, β=71.80°, Triclinic P
c=17.79 Å γ=66.71°
Thanks in advance!
I have performed LC MS/MS analysis of pooled patients' plasma and have identified one protein of interest. The database search of the MS/MS spectrum was performed with proteome discoverer software. The identified protein of interest after database search gave a score of 4.5 and number of unique peptide identified is 1. Can I report the protein based on such a result? Any reference link will be of great help where such situations are reported and validated.
I am working on a project examining teacher's role in supporting student SRL. This clearly can include many things such as implementing interventions, utilizing teaching practices to foster or teach SRL skills (e.g., provide effective feedback, engage students in self-assessment), designing effective assignments (e.g., open-ended, long term projects), and creating supportive learning environments. I have read some really great review papers and many manuscripts, but my database searches seem to miss the mark (likely due to terminology) and I feel as though I am missing something. I am early in this project and if you know of any resources you think that I might want to read or include as I work on this project, I welcome your suggestions. Thanks a lot!
I plan to perform systematic review and I need to establish databases that will be searched for. I found that majority of researchers screen for two databases (PubMed and Medline). According to NIH website PubMed gives more results and additionally includes those from Medline:
The question is whether it makes sense to search for Medline database?
I need to search the NCI database and i can only find the MiniMayBridge and the sample satabases and can't find the option to browse and search other databases. I'm using Discovery studio 2.5.5. thank you
as i know inverted index consist of keywords and the document identifiers contain this keyword and the search on this index structure is sequential for single keyword search but if i want to search for multi keyword in this index . will divide this multi keyword for single keywords and search for it sequentially . iam thinking to use map-reduce algorithm to make this search in parallel.
Are there any values/references for how low/high the False discovery rate should/can be? For example, using Mascot search with the automatic decoy database for small to medium sized samples (100-10,000 MS/MS scans). The sample is searched e.g with all entries using SwissProt. The FDR is set by default to 5% (significant threshold). The automatic decoy database is also searched with all entries using SwissProt. How low/high can the FDR for the decoy database can be? For the small to medium sized samples, I obtain values from 20-80% FDR in the decoy base, which seems relatively high to me. How big has a sample to be that a decoy database search is required in MS/MS scan numbers? What makes a sample small, medium and big? Thanks for your help in this matter, Martina
Is there a way to search in the Acknowledgements field of “all” published scientific papers? I can’t find such a delimiter in Web of Science (but maybe I just don’t know where to find it). Do you know of any other database / search engine that will let me do this?
I'm looking to quantify the use of various words and phrases.
Can someone direct me to sample quantitative data sets that can be used to teach simple descriptive statistics in an online course?
I am looking to explore the association of genes with clinical outcome,
I tried a bit the Oncomine site, however I will be happy to know about alternatives.
It is known that cancers are associated with translocations of different chromosomal arms.I want to find epigenetic marks like histone methylations,acetylations, DNA methylations etc in fusion gene products. I have tried searching UCSC genome browser but no luck yet.
I am working on detecting different compounds present in my sample. I ran in using LC-MS (Agilent QtoF). I am only used to use Metlin as my database for searching compounds using my m/z. But now I also have to search for any toxic compounds. Is there other database that may be useful regarding this matter?
I have a database with millions of records stored in it. I want to implement Search and Functionalists in My db with some AI and data mining techniques and methods.
Suggest me Some Algo, Methods and Techniques for implementing this with AI. So that it becomes more and more efficient as the time passes.
It would be nice if anyone suggest with keep in mind that I am working with Python Frameworks and PHP.
I am interested in detection of all protein isoforms arising from alternative splicing events. To do this, I would like to set up database searches to account for all isoforms by parsing unique peptides separately from razor peptides common to 2 or more isoforms. In the end it would result in separate protein assignments for unique isoforms and for common isoforms. Does anyone do this already, and if so, is there a way to set database search parameters in such a way as to do this quantitatively, i.e. unique isoform 1 protein ratio, unique isoform 2 protein ratio, protein ratio arising from common peptide isoforms 1 and 2, etc.? Even standard parsimony assumptions do not always result in what I consider accurate protein ratios. For instance, looking at a protein where isoform 2 is subsumed by isoform 1 I've detected isoform 1 unique peptides at one ratio and common 1/2 peptides at a very different ratio. By standard parsimony I would conclude that only 1 is present, but by the peptide ratios it is clear that 2 is also present but at a very different ratio than isoform 1. I've read several papers touching on these issues, but haven't yet found anything that fully addresses them.
Hi to all. I do not have an ESI-MS coupled to an hplc, and I need to analyze a band excised from a gel. Once I have desalted the tryptic digest, how can I set the database search considering that tryptic peptides have a +2 or +3 charge states? In MASCOT (Matrix science) I have only the possibility to perform research of peptide mass finger printing setting MH+ charge states, and to perform a search against MS/MS data.
I see a considerable convergence in database searching. Some papers reported they searched for example Pubmed, Scopus and Embase. Others said Scopus covers Medline, and it is not unnecessary to search Pubmed. I saw some papers reported they searched above databases together with web of science.
I would like to know which databases I should search with least overlapping results.
How to determine whether the entire search process, starting with the initial interview, can or should be improved.