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--- orcs:curation_guide [2019/06/27 09:08]
jenn [High-Throughput Screen Curation]
+++ orcs:curation_guide [2020/08/19 10:56]
jenn [Curation Questions and Answers]
@@ Line 8: / Line 8: @@
   * [[orcs:curation_guide:publication_queue|Publication Queue]]
   * [[orcs:curation_guide:datasets|Datasets]]
-  * [[orcs:curation_guide:metadata_terms|Manually Curated Fields]]
+  * [[orcs:curation_guide:metadata_terms|CRISPR Screen Metadata]]
+  * [[orcs:curation_guide:contacting_authors|Contacting Authors]]
-[[:orcs:curation_guide|Back to ORCS Curation Guide]]
 ===== Curation Questions and Answers =====
-  - **Should we curate all interactions in a paper?**
+  - **Are we curating all CRISPR screens and mutants? **
-    * We capture all interactions in a paper, even if they are not the main focus of an experiment and have been curated previously. For example, in Fig. 3 of [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15608614&query_hl=4&itool=pubmed_DocSum|PMID: 15608614]], the authors were looking at the effects on the TOM complex after depletion of MIM1. Even if there aren't any interactions being added for MIM1 based on this figure, the interactions between the subunits of the TOM complex (e.g. TOM70, TOM40, etc.) should be added under 'co-purification'.  We also curate interactions found in supplementary files.
+     * Currently our focus is on capturing genome-wide CRISPR screens. Occasionally screens performed with targeted libraries will be captured if we run across them in the course of literature review. In the future our scope may expand to more comprehensively capture these targeted screens or even single mutant data.
+  - **Why does the screen show fewer hits than mentioned in the text? **
-===== BioGRID Team Members, References, and Funding Details =====
+     * ORCS curators load genes based on the identifiers provided by the authors in supplemental text, these can include gene symbols, aliases or gene IDs. Whenever possible ambiguous IDs are mapped to a single identifier but genes that cannot be clearly mapped to an identifier will be captured/displayed but will not contribute to the overall hit count which could result in small discrepancies between screen hit number and those reported in the literature.
-For more information on the BioGRID and the history of the BioGRID, a full list of our publications, team members, and funding sources can be found on our [[aboutus|About Us Page]].
+  - **Why would a particular hit gene have a low ranking? **
+    * Scores used for gene ranking are not always the criteria used to determine hit status by an author. Authors may use an enrichment/depletion score to order genes but use an associated confidence value to determine the hit status of a gene. ORCS automatically displays hit genes first for a screen. In particular, screens that identify both the most enriched and most depleted genes in a single screen are likely to have both high ranking and low ranking genes as hits depending on analysis method.
+===== ORCS Team Members, References, and Funding Details =====
+For more information on ORCS and the history of the BioGRID, a full list of our publications, team members, and funding sources can be found on our [[aboutus|About Us Page]].