--- # DIRECTIONS # As your first curation assignment, read the paper Tang, Su et al., 2017 (doi: 10.1093/jxb/erw425). # Create your own yml file based on the blank and annotated templates below. # Name your new file "Tang_Su_2012_practice.yml." # When you are done, compare your yml file to the Answer Key provided below. --- # BLANK TEMPLATE scientific_name: classical_locus: gene_symbols: - gene_symbol_long: gene_model_pub_name: gene_model_full_id: confidence: curators: - comments: - phenotype_synopsis: traits: - entity_name: entity: references: - citation: doi: pmid: - citation: doi: pmid: --- # ANNOTATED TEMPLATE scientific_name: # REQUIRED; the two-word binomial, e.g. Glycine max classical_locus: # Name of locus if available from classical genetic studies. Delete this line if no locus is mentioned. gene_symbols: - # Abbreviated gene name as listed in the paper. It should be formatted like "GmNNC1." - # If there are multiple names for one gene, enter them on separate lines with the most common name listed first. - # If more than one gene is described in the same paper, paste another copy of this template at the bottom of your document and fill it in for the second gene. gene_symbol_long: # The long-hand version of the gene_symbol acronym, e.g. "Nodule Number Control 1" (do not include the prefix Glycine max). gene_model_pub_name: # REQUIRED; This should be listed in the publication, e.g., Glyma02g17170.2, SoyW82_02G152800.1, or Glyma.02G152800, depending on the annotation version. # If the paper has no gene model name (rather, has a gene symbol plus sequence) try one of the search methods described at the bottom of this document. gene_model_full_id: # REQUIRED; The gene name in Legume Information System. It looks like "glyma.Wm82.gnm2.ann1.Glyma.12G078000". # Find it by entering your gene_model_pub_name into the "Identifier" search box on this website: https://www.legumeinfo.org/tools/search/gene.html confidence: # A value from 1 to 5 showing how strong the evidence for the gene's function is. # See the bottom of the document for guidance on assigning a confidence level. curators: - # Put your name here comments: - # If the information is available, briefly describe the function of the gene, what genes it interacts with, and how it is regulated. - # If the gene affects/is affected by another gene you have curated, include the name of the yml file which discusses the interacting gene. - # E.g. "miR172c cleaves the protein product of NNC1, allowing ENOD40 to be transcribed. miR172c is negatively regulated by NARK (see Searle_Men_2003.yml)." phenotype_synopsis: # Briefly describe the phenotype, e.g. "NNC1 is a transcription factor that negatively regulates nodule number by repressing GmENOD40." traits: # REQUIRED; at least one "entity" ontology accession describing the function of the gene. Find ontologies by searching this database: https://www.ebi.ac.uk/ols/ontologies - entity_name: # The name of the ontology accession, e.g. "nodulation" entity: # The ontology accession code, e.g. "TO:0000898", with "TO" indicating the Trait Ontology - quality_name: # Optional; quality ontologies can be used to describe properties of the trait, e.g. "premature." quality: # Quality ontology codes usually begin with "PATO" - relation_name: # Optional; Relations ontologies can be used to describe the effects of the trait, e.g. "negatively regulates." relation: # Relations ontology codes begin with "RO" - entity_name: # Additional ontologies can be added to describe other functions, e.g. "regulation of biological process involved in symbiotic interaction" entity: # Code of additional ontology. # You can add more lines describing the qualities and relations of your additional ontology entities. references: # REQUIRED; At least one citation with its doi or pmid. Ideally, include several citations. - citation: # The primary paper you extracted information from. Use the "LastName, LastName et al., YEAR" format, e.g. "Wang, Wang et al., 2014" doi: # the bare doi (omit https://doi.org/), e.g. "10.1105/tpc.114.131607," not "https://doi.org/10.1105/tpc.114.131607" pmid: # Either search for your paper on PubMed, or use the "get_citations.pl" script in a new document to find pmid based on doi (or vice versa!). E.g. "25549672." - citation: # Additional citation of a paper providing more information. doi: pmid: --- # ANSWER KEY scientific_name: Glycine max gene_symbols: - GmCIF1 # This paper discusses both GmCIF1 and GmC/VIF2 in detail, so there is a second version of this template below for GmC/VIF2. gene_symbol_long: Cell Wall Invertase Inhibitor gene_model_pub_name: Glyma17G036300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036300 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Ectopic expression and RNAi silencing show that CIF1 has a role in suppressing extracellular invertases. - Silencing of CIF1 increases seed weight as well as protein and starch content. - CIF1 is activated by ABA signaling, draught, and senescence. - CIF1 is strongly expressed in flowers, mature leaves, and developing seeds. phenotype_synopsis: CIF1 is an invertase inhibitor which represses CWI (cell wall invertase). traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed size entity: TO:0000391 - entity_name: protein content entity: TO:0000598 - entity_name: starch content entity: TO:0000696 references: - citation: Tang, Su et al., 2017 doi: 10.1093/jxb/erw425 pmid: 28204559 - citation: Su, Han et al., 2018 doi: 10.3390/ijms19082395 pmid: 30110937 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmC/VIF2 gene_symbol_long: Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 gene_model_pub_name: Glyma17G036400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036400 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Ectopic expression and RNAi silencing show that C/VIF2 has a role in suppressing extracellular invertases. - Silencing of C/VIF2 increases seed weight as well as protein and starch content. - C/VIF2 is activated by ABA signaling, draught, and senescence but suppressed by fungal infections. - It is most strongly expressed in flowers, roots, and developing seeds. phenotype_synopsis: C/VIF2 is an invertase inhibitor which represses CWI (cell wall invertase). traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed size entity: TO:0000391 - entity_name: protein content entity: TO:0000598 - entity_name: starch content entity: TO:0000696 references: - citation: Tang, Su et al., 2017 doi: 10.1093/jxb/erw425 pmid: 28204559 - citation: Su, Han et al., 2018 doi: 10.3390/ijms19082395 pmid: 30110937 --- # ADDITIONAL RESOURCES # To find or check the validity of your gene_model_pub_name: # First, search the gene name on Soybase. E.g. enter "NNC1" into the search bar here: https://www.soybase.org/search/index.php. # Next, search the gene name in NCBI. E.g. enter "Glycine max NNC1" into the search bar here: https://www.ncbi.nlm.nih.gov/gene/ # Scroll until you find the FASTA file for your gene of interest. Copy and paste the complete sequence into Funnotate (https://funnotate.legumeinfo.org/) # Click "Upload Seqence(s)," then "Begin Annotation." Click on the little hammer and wrench icon to load a family tree. # Examine the soy gene_model_full_ids close to the highlighted USR. The gene_model_pub_name is the segment at the end of the gene_model_full_id. # Compare the gene_model_pub_name from Soybase to the output from Funnotate. # Google the gene_model_pub_name to confirm that the name is used in scientific literature. # Guidance on confidence levels: