Exercise No. 9: Medical Scientific Databases PDF

**Exercise no. 9** **Familiarizing the students with the basic medical scientific databases** **Theory** **Student:** - **knows the application of the most popular medical databases - NCBI, Google Scholar,** - **knows the names of other, paid scientific databases.** **NCBI - National C...

**Exercise no. 9** **Familiarizing the students with the basic medical scientific databases** **Theory** **Student:** - **knows the application of the most popular medical databases - NCBI, Google Scholar,** - **knows the names of other, paid scientific databases.** **NCBI - National Center for Biotechnology Information (USA) -- part of The National Library of Medicine -- a scientific institution that gives access to several tens of databases from biotechnology, biomedicine, and genomics such as e.g. GenBank, PubMed, and BioProject, available online.** **1) ClinVar Base -- collects data on genome differences, mutations, and their relations with the general health condition (https://www.ncbi.nlm.nih.gov/clinvar/)** **2) Base of clinical tests conducted worldwide sponsored by both the private and public sectors ([[https://classic.clinicaltrials.gov/]](https://classic.clinicaltrials.gov/)). The database allows for the finding of ongoing or finished clinical tests during the recruitment of probands. The database contains the current status, results, and stage of advancement of a given clinical test.** **3) PubMed -- a database of Biomedical scientific articles (https://pubmed.ncbi.nlm.nih.gov/)** **Google Scholar -- a search engine for scientific articles made by Google Inc. It was launched in November 2004 (https://scholar.google.com/)** **There are also paid (licensed) scientific databases available, including:** - **Polish Medical Bibliography -- a part of the Stanisław Konopka Main Medical Library, containing scientific works created since 1991** - **Scopus -- a database run by the Elsevier Publishing Company created in 2004 (available in Poland since 2012) which brings together information about published scientific works, conference materials, and patents,** - **Web of Science -- a platform ensuring access to numerous databases containing bibliographical data and citations from academic journals, conference materials, and other documents.** **Practice** **Student:** - **can find basic information in the NCBI and Google Scholar medical databases,** - **can use advanced search options/search filters in the above-mentioned databases,** - **can compare search results from different databases.** **Remarks for exercises 1-5:** **Answers should be written in the assigned spaces and/or pasted into the worksheet as screenshots. Headings under which the appropriate screenshots must be pasted are marked in red.** **Sample exercise solved along with a description of individual steps.** **The *ercc2* gene is connected with the *Xeroderma pigmentosum* group D genetic disorder, which occurs as a result of a genetic dysfunction causing a decreased ability to repair DNA damage caused by UV light.** **Directions: go to https://www.ncbi.nlm.nih.gov/clinvar ( NCBI, ClinVar database) and find a variant of the *ercc2* gene causing premature termination of protein synthesis. Termination is identified by the abbreviation "Ter" while the consequence of the termination (the non-functional protein) is identified as "nonsense"** **Solution:** **1516 variants of the *ercc2* gene have been found. Then the results were filtered marking nonsense as a molecular consequence (23 results)**  **After clicking a given mutation description an image appeared showing the details of this mutation:**  **Exercise no 1** **In the ClinVar database:** a. **find the SRY gene. Determine the number of polymorphisms (sequence variants) of the SRY gene** **Screenshot of the searches for SRY gene variants** **.................. variants of the gene have been found.** b. **Find information on the following point mutation of the SRY gene: 380A\>G (p.Tyr127Cys). To find the mutation from among the presented variants (from a above) copy this mutation (Ctrl +C), on the search engine page press Ctrl +F (the search window will appear) and then paste the sequence (Ctrl +V) and find it by pressing Enter.** **Screenshot of the part of the list with the search for the mutation** **Screenshot with details regarding the 380A\>G (p.Tyr127Cys) mutation** **List the molecular consequences of this mutation:** **.................................................................................................................................** **Exercise no. 2** **In a clinical trials database:** a. **find the information regarding the number of clinical studies on SARS-CoV conducted by Pfizer by putting in the search terms as seen in the screenshot below:** **Screenshot of the search for clinical studies** **.................. clinical studies have been found.** b. **Please find clinical studies in Poland which are in the recruitment phase and concern diabetes. How many such studies are currently ongoing? First, find all clinical studies and then use the filter \"Recruiting\".** **Screenshot of the search for clinical studies during the recruitment phase** **.................. clinical studies during the recruitment phase have been found** c. **Please check if there are any current studies in Poland regarding COVID-19. What filters should be used?** **Screenshot of the search results for clinical studies** **.................. ongoing clinical studies have been found.** **Exercise no 3** **In the PubMed database** **a) Find free publications containing information on the ORF3 protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Using advanced search options, show only review articles. The search terms/filters should be entered as can be seen on the screenshots below to then be able to determine the number of publications found.**   **Screenshot of search results** **.................. articles fulfilling the given criteria have been found.** **b) Using the appropriate filters find free and Polish publications regarding the C-reactive protein. The terms/filters should be entered as seen in the screenshots below and then the number of publications found should be specified.**   **Screenshot of search results** **.................. articles fulfilling the given criteria have been found.** **Exercise no 4** **In the Google Scholar database, using advanced search options (as seen on the screenshots below) find information/publications regarding SRY, with the phrase „sex determination region" without the word disease, from the years between 2015 and 2020. Please specify the number of publications found.** **Na ekranie: My Profile, My library, alerts, data, advanced search, settings** **:**  **Na ekranie: advanced search, find articles, with all words, with the phrase, with at least one of the words, without the words, in which the words are -- in any place in the article, in the article title** **display works of whose author is** **display works published here:** **display works from the period:** **Screenshot with the search results** **.................. articles fulfilling the given criteria have been found.** **Exercise no 5** **Database comparison.** **Using the advanced search options both in the PubMed database as well as Google Scholar find all articles about ORF3 with the term Covid 19, without the words „ ORF3 gene", that were published in 2020.** **Screenshot of search results from PubMed** **Screenshot of search results from Google Scholar** **PubMed:......................publications** **Google Scholar:...................... publications**