GlyGen Detailed Testing Instructions GlyGen detailed testing is more comprehensive and intensive than the Quick Testing. The detailed testing not only includes data issues but also interface, display and content issues. In detailed testing GlyGen search, list and details, data, API and SPARQL pages are tested including the search pages. Below are bullet points that will help in doing a detailed test. The detail test is done primarily on beta and prd interfaces or told otherwise. See the GlyGen subdomains document if you don’t know the subdomain interface you are asked to test. To access GlyGen Tst and Dev servers from your personal PC and or laptop, connect to GW VPN. Download VPN - https://it.gwu.edu/virtual-private-network-vpn | Instructions - Create the testing report by giving an appropriate name that contains data, version , tester’s name etc and upload to the recommended location. Provide the URLs and screenshots for the issues Upload the report to - /data/projects/glygen/documentation/test_results/ GlyGen Search and Advanced Pages -> Explore Glycan, Protein and Glycoprotein (https://glygen.org/)) Data page - https://data.glygen.org/ API - https://api.data.glygen.org/ SPARQL or https://sparql.glygen.org/ To test DEV and TST server, replace $server with the server name here - https://$server.glygen.org/ To do detail testing CHECK ##### Protein, Glycan and Glycoprotein Simple Search Page (All searches, text and links) ----- To test, search the protein, glycoprotein and glycan simple search pages by using all the searches and examples shown on the interface. Use different search examples from the dataset to test more. Check for the error or issue in the respective API. Report any issues/errors if the search field generates error when searching by the displayed example. ----- Examples * Good J3QPP2-1 * Good Q9BUM1-1 * Good Q9NPJ8-1 * Good Protein, Glycan and Glycoprotein Advanced Search Page (All searches, text and links) ----- To test, search the Advanced Search pages of Glycans, Protein and Glycoprotein using the examples shown on the interface including the examples in the drop down or the sliders. Use different search examples from the dataset to test more. In advanced search pages, some fields allows to use valid combinations to get results. For eg searching of Human proteins that a particular pathway of GO ID. Search using combinations. Enter multiple accessions in search fields where applicable, to test the functionality eg UniProtKB Ac in Protein Advanced search. Ensure all examples on the advanced search pages are working Check whether the help links are active and working Check whether the info displayed in the help text is correct and uptodate. Report any issues or errors found ----- Examples * Good J3QPP2-1 * Good Q9BUM1-1 * Good Q9NPJ8-1 * Good List pages (Links, pages, download) ##### Protein Detail Search in Protein advanced search using these examples - P14210, P27958-1, P26662-1, P59594-1, P0DTC-2, Q08048-1, P17945-1 Protein and Glycan detail pages (All data sections and links) ##### ----- J3QPP2-1 * In section isoform: clicking the “UniProtKB Accession Length:” link leads to the main uniprot page but not specifically the length section * Isorform accession link also goes to the main page, not the isoform section Q9BUM1-1 * Same issue with isoform and length not finding specific uniprot section * Cross-reference page for OMA is invalid: https://omabrowser.org/oma/group/LVPWVVH/ Q9NPJ8-1 * In Alignment tab page (from Isoforms section), the left sidebar overlaps the results * In Expression section, missing certain tissues (example Kidney cancer, sig exp) * Cross-reference page for OMA is invalid P27958-1 * In disease section, Glygen links lead to a “Not Found” error * Unclear what the exact links should be * Tried searching in data.glygen.org for both the disease name and GLYGDS number but neither had results * When searching in Glygen.org for the disease, other proteins with this disease listed contain a link for OMIM * Examples: https://www.glygen.org/protein_detail.html?uniprot_canonical_ac=P25054-1&listID=d5fda7d3228c762c5db1356e6441efde&gs=Hepatocellular%20carcinoma * https://www.glygen.org/protein_detail.html?uniprot_canonical_ac=P08581-1&listID=d5fda7d3228c762c5db1356e6441efde&gs=Hepatocellular%20carcinoma * Should the links for P27958-1 be for OMIM, not data.glygen.org? P26662-1 * Same issue as P27958-1 above in Disease section, Glygen links do not work P59594-1 * In General section: record for the RefSeq Accession has been removed by NCBI * Link https://www.ncbi.nlm.nih.gov/protein/NP_828851.1 * I believe this is the new link for this protein https://www.ncbi.nlm.nih.gov/protein/AAT52330.1 * Same issue in Disease section, linkout to Glygen does not work P0DTC-2 * In Disease section, the Glygen link DOES work * Working link: https://data.glygen.org/GLYDS000490 * In previous example P59594-1, the link is for GLYDS000489 Q08048-1 * In Cross References, OMA link does not work * https://www.glygen.org/protein_detail.html?uniprot_canonical_ac=Q08048-1&listID=9b3d603909f6e7d1dcab478b6483ae12&gs=Q08048-1 * When searching for this group in OMA, Mus musculus was not a species listed for this group * https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=GIPTQTN P17945-1 * In Cross References, same issue as Q08048-1, OMA does not list Rattus norvegicus for this group Data Page (Datasets, downloads, BCOs, FAQs, Release History) ----- � Check whether all datasets have images/tables displayed � Check whether the filters work on not � Click on several datasets to ensure they have sample view page � Check description and sample table is displayed on the sample view page � Check that datasets can be toggled to different version when the option is available � Check BCOs and readme links display the content. � Check the download datasets options words and shows all the entries. � Check the other menu links such as FAQs, Release history � Check the API, SPARQL and Portal links work or not * Portal link does not generate a new page, it only reloads the same page I am currently on. Seems that it is broken? � Report any issues/errors API Page (All APIs, Links) ----- � Check whether all APIs can be successfully executed by using the given examples * The example query for “Glycans synthesized by enzyme/protein X” and “Glycoproteins reported in species X” do not load * Page unresponsive error * For Glycans synthesized by enzyme/protein X… also tried {"uniprot_canonical_ac":"Q9H3H5-1"} but same error resulted * For Glycoproteins reported in species X… Also tried {“tax_id”:10090, “evidence_type”:”both”} but same error resulted � Check if the data displayed is correct and as per the API � SPARQL Page � Check all the links are working � Search the sample queries for result � Check if the information is displayed in all the formats SPARQL Page (All Queries and Links) ----- Notes � If you find issues, double check the issues � Check the data issues in same server API and datasets in dev server before reporting. Copy the datasets locally before opening) � Check for grammar and types � Report all issues in a document with as much details as possible (server, browser, data, page, version, URL (most important), screenshots etc) � Mention the version, server, date and name etc in the details. Tested the example query on SPARQL page List Page � To test list pages search using the simple and advanced search pages of protein, glycoprotein and glycan examples. � Upon successful searching in the search pages, list page appears that contains the summary of the search, number of search results and tables containing either protein or glycan accessions. � Check whether the search summary is correct and as per the search executed, the table contains the correct information, prev and next page options work and the list page can be downloaded. � Check whether the downloaded file contains all information shown in the list page � Check and see whether the same info is also shown in the API and dataset or when there is an error for verification � Make sure to check both glycan and protein list page. Detail Page � Check all the links are working and correct for all sections of protein and glycan detail all pages. Eg UniProtKB ac link should open the UniProtKB page for that accession. � Check whether the data displayed is correct. Eg If glycan in N-glycan, then the image should be of N-glycan � If the data has error check the data in the APIs and relevant datasets � Check header, footer and menu links and functionality. � For some accessions not all sections will have data. Check to ensure there is genuinely no information available for that section. � Ensure the data, page and sections are displayed optimally. � Report errors/issues Upload the report to - /data/projects/glygen/documentation/test_results/