I. Expr_pattern curation procedure. Gene Expression data were extracted from Result section, sometimes from Tables or Figure legends. Method information can be found from "Material and Methods". I have a template .ace file for Expr_pattern, all I need is to fill the data-fields. The text entered as Method and Remark should follow my template.txt file, making them easy to search later. Each experiment is a new Expr_pattern, unless the description make it really hard to separate two experiments. Usually I copy-past from PDF or HTML, then edit to get rid of "extra" words, such as author comments or speculations. The text were pasted under "Subcellular_localization" or "Pattern", depending on the content. 1.1. Figure out what Gene is used. Usually check CGC_name and compare the paper with current WormBase release. Enter Gene ID. 1.2. Method If GFP/LacZ construct is used, I try to get the following information: 1.2.1. What kind of fusion -- Translational/transcriptional/promotor. Fill information under "Reporter_gene".. Translational fusion: When reporter_gene is fused in-frame to coding sequence. Or if author said it is translational fusion but did not provide furthur info. Transcriptional fusion: When reporter_gene is not fused in-frame to coding sequence. Or if author said it is transcriptional fusion but did not provide furthur info. Promoter fusion: When reporter_gene is fused directly to promoter sequence, no coding sequence included in the construct. 1.2.2. What is the driving sequence -- PCR primers, start/end nucleotides (such as -1250 to + 40) (If information is enough to create a Sequence object later, Label as "--precise ends" at the end of Reporter_gene field. This is ?Text.) 1.2.3. Check if there is a Transgene used, integrated or not, create the Transgene and XREF to this Expr_pattern. If Antibody is used. check whether it is new antibody, if yes, create a new object. If already exist, XREF it to this Expr_pattern If In_situ, RT_PCR, Northern or Western is used, enter these tags. Unless there are more info, most of the time, just the method tag. 1.3. From "Pattern" entry I extract and XREF to Anatomy_term (used to be Cell, Cell_group) and Life_stage information. 1.4. If there are other information, fill Remark field. See template.txt for all possible cases. 1.5. Enter reference as Paper ID. 1.6. After curation for all Expr_pattern is done, clean up. Check .ace file in empty database for correct syntax. 1.7. Check .ace file using AceChecker.pl script, to convert Cell objects to Anatomy_term, and make sure Gene ID, Paper ID, Life_stage are not wrong. 1.8. Check .ace file in WS_release, make sure no extra XREF objects were created by looking at total number of objects in each class. //Expr_pattern model (WS139) ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern CDS ?CDS XREF Expr_pattern // for coding genes Sequence ?Sequence XREF Expr_pattern // for clones??? Pseudogene ?Pseudogene XREF Expr_pattern // new [030801 krb] Clone ?Clone XREF Expr_pattern Protein ?Protein XREF Expr_pattern Protein_description Text // stores information for Expr_patterns // with unknown antigens [031105 krb] Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier Cell_group ?Cell_group XREF Expr_pattern #Qualifier Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition Subcellular_localization ?Text Type Reporter_gene ?Text In_situ Text Antibody ?Text Northern Text // added for Wen [krb 030425] Western Text // added for Wen RT_PCR Text // added for Wen Pattern ?Text Picture ?Picture XREF Expr_pattern Remark ?Text #Evidence Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Transgene ?Transgene XREF Expr_pattern Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining // added [031120 krb] Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) //Curation Template for Expr_pattern Expr_pattern : "Expr" Reference "" Gene "" Cell "" Cell "" Anatomy_term "" Life_stage "" Life_stage "" Antibody Antibody_info "" Reporter_gene "" In_situ Northern Pattern "" Subcellular_localization "" Remark "" Transgene "" Curated_by "Caltech" //The following are the controlled vocabulary for Expr_pattern objects. Life_stage "blastula embryo" Life_stage "gastrulating embryo" Life_stage "enclosing embryo" Life_stage "elongating embryo" Life_stage "fully-elongated embryo" Life_stage "embryo" Life_stage "L1 larva" Life_stage "L2 larva" Life_stage "L3 larva" Life_stage "L4 larva" Life_stage "adult" Remark "New symbol: " Remark "Reporter gene fusion type not specified." Remark "Gene_regulation: " --precise ends. Remark "Injection marker: pRF4." Remark "Type: RNase-Protection Assay." Remark "Type: Phage_hybridization." Remark "Type: mammalian cell transfection." Remark "No detailed description on cellular expression patterns." ---------------------------------------------------------------------------------- II. Transgene curation. Transgene details can always be found from "Materials and Methods". I have a Transgene .ace template. I type or copy-paste corresponding information to the data fields. Before creating a new object, check whether it already exists in wormbase, using its name. 2.1. Identify Transgene name. Usually they are like "syIs10" or "eEx1986", if no name, call it cgc1234Is1, or pmid12345678Is1 ... 2.2. Identify the driving promoter. Enter Gene ID. Identify reporter gene, enter Gene ID or reporter_product info. 2.3. Write the summary, following my Transgene template and template.txt. 2.4. Identify whether and how it was integrated. Enter the info. 2.5. Identify whether and where it is mapped. Enter Map. 2.6. Identify which Lab created it or used it, enter Location(Lab ID). (Do not distinguish which Lab originally created it. The Location field indicate where you can find this Transgene.) 2.7. Enter Reference. 2.8. If there are extra info, enter Remark. 2.9. Check .ace file in empty database for correct syntax. 2.10. Check .ace file using AceChecker.pl to make sure Gene ID, Paper ID, are not wrong. 2.11. Check .ace file in WS_release, make sure no extra XREF objects were created by looking at total number of objects in each class. //Transgene model (WS139) ?Transgene Evidence #Evidence Summary UNIQUE ?Text //Searchable description of the transgene Driven_by Driven_by_CDS_promoter ?CDS XREF Drives_transgene Text //driving promoter Driven_by_gene ?Gene XREF Drives_transgene Reporter_product GFP LacZ Other_reporter ?Text Gene ?Gene XREF Transgene_product Text CDS ?CDS XREF Transgene_product Text Isolation Author ?Author Clone ?Clone XREF Transgene Text //injected clone conc. Fragment Text Text //injected DNA fragment conc. Injected_into_CGC_strain ?Strain Injected_into Text // for strains not available in CGC Integrated_by UNIQUE Gamma_ray X_ray Spontaneous UV Particle_bombardment Not_integrated Other_integration_method Text Location ?Laboratory #Lab_Location //Which Labs have the transgene. Strain ?Strain XREF Transgene //All strains in CGC with the transgene. Map ?Map #Map_position Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Phenotype ?Text //Phenotype should be described as "Unc. With other ..." Rescue ?Gene XREF Rescued_by_Transgene ?Allele XREF Rescued_by_Transgene Expr_pattern ?Expr_pattern XREF Transgene //Related Expr_pattern Gene_regulation ?Gene_regulation XREF Transgene Reference ?Paper XREF Transgene //papers refered to the transgene. Species UNIQUE ?Species // added by krb for consistency with other classes 021030 Remark ?Text #Evidence //More comments on the transgene //Curation Template for Transgene Transgene : "" Summary "[]" Driven_by_Locus "" Reporter_product "?GFP" Strain "" Map "" Integrated_by "?Gamma_ray" Location "" Reference "" Remark "" //Transgene controlled vocabulary Remark "Conflicting mapping info: " Remark "Clone = " Remark "Mapping info: " Remark "Also known as ... in cgc....." Remark "New name: " -------------------------------------------------------------------------------- III. Antibody curation Antibody information usually can be found from "Materials and Methods". 3.1 Check whether this antibody already exist in WormBase. I look for all antibodies against the gene, then compare the author, the antigen. the name ... 3.2 If a new antibody. Create the object name such as cgc1234:abc-1. Enter Other_name (the name used by authors). 3.3. Identify Animal. 3.4. Identify antigen, If recombinant protein, write down in "Protein" field nucleotide sequence. PCR primers or amino acids of start/end. If peptide, write down in "Peptide" field peptide sequence. 3.5. Polyclonal or monoclonal. 3.6. Write summary. How the antibody was created. 3.7. If there are extra info, enter as Remark. 3.8. Enter Location/Laborary. 3.9. Enter in Remark orginial created Lab info. 3.10. Enter reference. //Antibody model (WS139) ?Antibody Evidence #Evidence Summary ?Text #Evidence Other_name Text Gene ?Gene XREF Antibody CDS ?CDS XREF Antibody // might not be needed in the long run Clonality UNIQUE Polyclonal Text Monoclonal Text Antigen UNIQUE Peptide Text Protein Text Other_antigen Text Animal UNIQUE Rabbit Mouse Rat Guinea_pig Chicken Goat Other_animal Text Expr_pattern ?Expr_pattern XREF Antibody_info Gene_regulation ?Gene_regulation XREF Antibody_info Location ?Laboratory Reference ?Paper XREF Antibody Remark ?Text #Evidence //Curation Template for Antibody Antibody : "[cgc]:" Other_name "" Summary "" Locus "" Animal "" Clonality "" Protein "" Peptide "" Location "" Reference "" Remark "Original publication: cgc."