Difference between revisions of "RNAi"

Latest revision as of 20:29, 30 July 2019

Archived RNAi documentation may be found here

1 RNAi Curation Mission Summary
2 RNAi Data Model
3 RNAi annotations in CitaceMinus
4 RNAi Curation Standard Operating Procedure (SOP)
- 4.1 Minimum Requirements for an RNAi Object
5 RNAi Paper Flagging and Processing of SVM "Low" Results and Tracking
6 RNAi OA Postgres Tables (rna_*)
7 RNAi OA
8 *.ACE Dumper Documentation
- 8.1 Error Checks During Dump Process

RNAi Curation Mission Summary

The term "RNAi" stands for "RNA-interference" and refers to the targeted silencing of gene expression of a "target gene" via introduction of double stranded RNA (dsRNA) containing high degrees of sequence identity to the "target gene". In C. elegans, molecules of dsRNA may be introduced into the worm by a variety of different methods including direct micro-injection, soaking of worms in solution containing dsRNA, feeding worms bacteria that express dsRNA from a plasmid, and transgenic expression (within the worm) of dsRNA. For efficient and specific knockdown of gene expression, the dsRNA must have a minimum sequence identity with the target gene sequence. Any phenotype(s) resulting from the RNAi-mediated knockdown of a particular gene is thought to directly reflect the phenotype of a loss-of-function mutation in that gene, hence providing evidence as to the gene's biological function.

The goal of RNAi curation is to associate RNAi-mediated phenotypes with the target genes knocked down in RNAi experiments, as found in the literature pertaining to C. elegans and related species. There are some important things to consider when curating RNAi experiments. Some RNAi experiments are simple to curate as the strain is N2 (wild type genotype), only a single gene is targeted for RNAi, the phenotype is clearly stated, and the source and identity of the dsRNA is clearly stated by the authors. In many cases, however, the curation task is not so simple: there may be complex genotypes with multiple mutations in the strain receiving the dsRNA, multiple RNAi gene targets, complex genetic interactions, and/or missing descriptions from the authors as to controls, dsRNA delivery method, dsRNA identity, and/or phenotype directly resulting from the RNAi in question. Hopefully these issues will all be addressed below.

RNAi Data Model

This is the ?RNAi data model as of WormBase Release WS251:

//////////////////////////////////////////////////////////////////
//
// ?RNAi class
//
//////////////////////////////////////////////////////////////////

?RNAi   Evidence #Evidence
        History_name UNIQUE ?Text
        Homol Homol_homol ?Homol_data XREF RNAi_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
        Sequence_info   DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping
						  // 1st Text is DNA, 2nd is probe name
                       Sequence ?Sequence XREF RNAi  //links to a real Sequence object used in the experiment 
                                                     // such as yk clone; not UNIQUE anymore
                       Clone ?Clone XREF Used_in_RNAi       // Chris WS244
                       PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
                                                          // the experiment; not UNIQUE anymore
       Uniquely_mapped  //boolean; if present, signifies that ?RNAi object has a unique sequence 
                        // which maps to a single place in the genome
       Experiment      Laboratory ?Laboratory
                       Date UNIQUE DateType
                       Strain UNIQUE ?Strain
                       Genotype UNIQUE ?Text   //used when no Strain object exists
                       Treatment UNIQUE ?Text
                       Life_stage UNIQUE ?Life_stage
                       Temperature UNIQUE Int
                       Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
                                           Injection              //RL [010327]
                                           Soaking                //RL [010327]
                                           Transgene_expression   //RL [010327]
       Inhibits        Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
                       Gene ?Gene   XREF RNAi_result #Evidence           //RL [010327]
                       Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
                       Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
       Supporting_data Movie ?Movie XREF RNAi    // Lincoln, krb [010807]
       DB_info         Database ?Database ?Database_field ?Accession_number 
       Species         UNIQUE ?Species
       Interaction     ?Interaction
       Reference       UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of 
                                               // equates to a Study class for Will S
       Phenotype       ?Phenotype XREF RNAi #Phenotype_info
       Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info 
       Expr_profile    ?Expr_profile XREF RNAi_result // connection added during build [030106 krb]
       Remark          ?Text #Evidence
       Method UNIQUE   ?Method

Here is the WS251 ?Phenotype_info model:

////////////////////////////////////////////
//
// ?Phenotype_info Class
//
////////////////////////////////////////////

#Phenotype_info Paper_evidence ?Paper
                Person_evidence ?Person
                Curator_confirmed ?Person
                Remark ?Text #Evidence // specific remarks about the phenotype
                Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
                Quantity UNIQUE Int UNIQUE Int #Evidence
                Not #Evidence //This is being phased out but is needed for the next phase [06/08/10].
                Penetrance Incomplete Text #Evidence
                           Low Text #Evidence
                           High Text #Evidence
                           Complete Text #Evidence
                           Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
                Recessive #Evidence
                Semi_dominant #Evidence
                Dominant #Evidence
                Haplo_insufficient #Evidence
                Caused_by_gene ?Gene #Evidence
                Caused_by_other ?Text #Evidence
                Rescued_by_transgene ?Transgene
                Variation_effect Gain_of_function_undetermined_type #Evidence
                                 Antimorph_gain_of_function #Evidence
                                 Dominant_negative_gain_of_function #Evidence
                                 Hypermorph_gain_of_function #Evidence
                                 Neomorph_gain_of_function #Evidence
                                 Loss_of_function_undetermined_extent #Evidence    
                                 Null #Evidence
                                 Predicted_null_via_sequence #Evidence
                                 Probable_null_via_phenotype #Evidence
                                 Hypomorph_reduction_of_function #Evidence
                                 Predicted_hypomorph_via_sequence #Evidence
                                 Probable_hypomorph_via_phenotype #Evidence
                                 Wild_allele #Evidence
                Affected_by Molecule ?Molecule #Evidence // ?Molecule model Karen Yook
                EQ_annotations Anatomy_term ?Anatomy_term ?PATO_term #Evidence
                               Life_stage ?Life_stage ?PATO_term #Evidence
                               GO_term ?GO_term ?PATO_term #Evidence
                               Molecule_affected  ?Molecule ?PATO_term #Evidence
                Temperature_sensitive Heat_sensitive Text #Evidence
                                      Cold_sensitive Text #Evidence
                Maternal UNIQUE Strictly_maternal #Evidence
                                With_maternal_effect #Evidence
                Paternal #Evidence
                Phenotype_assay Strain ?Strain #Evidence
                                Treatment ?Text #Evidence
                                Temperature ?Text #Evidence
                                Genotype ?Text #Evidence
                Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence
                                       ES1_Very_hard_to_score #Evidence
                                       ES2_Difficult_to_score #Evidence
                                       ES3_Easy_to_score #Evidence

Here is the WS251 #Evidence hash model:

////////////////////////////////////////////////////////////////////////////////
//			      Evidence hash
////////////////////////////////////////////////////////////////////////////////

#Evidence Paper_evidence ?Paper                            // Data from a Paper
          Published_as ?Text                               //  .. track other names for the same data
          Person_evidence ?Person                          // Data from a Person
          Author_evidence ?Author UNIQUE Text              // Data from an Author
          Accession_evidence ?Database ?Accession_number   // Data from a database (NDB/UNIPROT etc)
          Protein_id_evidence ?Text                        // Reference a protein_ID
          GO_term_evidence ?GO_term                        // Reference a GO_term
          Expr_pattern_evidence ?Expr_pattern              // Reference a Expression pattern  
          Microarray_results_evidence ?Microarray_results  // Reference a Microarray result
          RNAi_evidence ?RNAi                              // Reference a RNAi knockdown
          CGC_data_submission                              // bless the data as comning from CGC
	  Curator_confirmed ?Person                        // bless the data manually 
	  Inferred_automatically Text                      // bless the data via a script
	  Date_last_updated UNIQUE DateType                // Stores last update timestamp
	  Feature_evidence ?Feature			   // Reference a Feature - eg for creation of isoform based on TEC-RED SL2
	  Laboratory_evidence ?Laboratory                  // Reference a Lab
	  From_analysis ?Analysis			   // Reference an analysis
	  Variation_evidence ?Variation			   // Explicitly record variation from which IMP manual GO annotations are made
	  Mass_spec_evidence ?Mass_spec_peptide
	  Sequence_evidence ?Sequence		           // for sequence data that hasn't been submitted to a public resource
	  Remark ?Text

RNAi annotations in CitaceMinus

These papers have >2000 RNAi objects and, therefore, did not get parsed into postgres tables for RNAi (a total of 59,656 RNAi objects stored in CitaceMinus) :

WBPaper00004402 (2287 RNAi objects)
WBPaper00004403 (2584 RNAi objects)
WBPaper00004651 (2479 RNAi objects)
WBPaper00005654 (14253 RNAi objects)
WBPaper00006395 (3230 RNAi objects)
WBPaper00024497 (10951 RNAi objects)
WBPaper00025054 (20709 RNAi objects)
WBPaper00029258 (3163 RNAi objects)

RNAi Curation Standard Operating Procedure (SOP)

In order to ensure consistency of RNAi curation across curators and WormBase releases, a set of standard procedures for RNAi curation are outlined below. The descriptions of these procedures include use of the two main methods for generating *.ace files for release submission: (1) the web-based CGI form for one-at-a-time RNAi object generation and (2) the batch form submission method.

Minimum Requirements for an RNAi Object

Regardless of which curation method you (the curator) choose, there are a set of minimum requirements in order to generate a complete RNAi experiment object:

1) A reference (e.g. WBPaperID)

2) A curator name

3) The sequence of the dsRNA used in the experiment to knockdown gene expression

4) A dsRNA delivery method (e.g. Injection) [Note: some authors omit this information. This can be curated arbitrarily and removed from the *.ace file once it has been generated]

5) A phenotype (observed or not_observed)

If any one of these five basic pieces of information are missing, the scripts that generate the *.ace file will fail, returning an error.

RNAi Paper Flagging and Processing of SVM "Low" Results and Tracking

We have been using SVM to flag papers that may contain RNAi data. These papers are given a probability score (High, Medium or Low) based on the SVM training set to reflect the possibility that they contain RNAi data to be curated. The High and Medium scoring papers are automatically added to the list of RNAi papers that are to be curated (on the Paper Editor) and the Lows are stored separately. The Low scoring papers must be manually checked by a curator and if the paper has "curatable" RNAi data, the curator must manually add that paper to the list. The Low scoring paper list is being checked approximately every 3 months (it is added to automatically every Monday at 2am based on SVM results). The following is the SOP for checking these papers and adding them to the list of RNAi papers to curate.

SVM Low's - SOP for checking papers

The file containing the papers with a low priority score (named "low") is stored on tazendra in the directory: /home/postgres/work/pgpopulation/svm/gary_rnai New papers are concatenated to this list. The curator checking the recently added papers must go back in the list to the most recent paper that has a "commented out" mark "//". This mark means that the list has been checked up to this point in the paper list....all papers after this mark need to be manually checked. When the curator is finished, they should "comment out" the last paper on the list so the next curator knows where to begin checking next time.

SVM Low's - SOP for adding papers to curation pipeline

After checking the "Low" papers, the ones that do conatin data must be added to the curation list. To do so go to the curator_first_pass.cgi on the web which is listed under "curation Forms" on the site map for tazendra. Add the appropriate number of the WBPaper id, for example just "00038308" without the WBPaper prefix, and click on the query button. Under "rnai" in the Gene Function section add the following comment in the curator box "SVM -LOW". When you hit "Flag" at the bottom of the page this paper will be added to the RNAi curation list and noted as an SVM with a low probability score.

SVM Low's - SOP for adding papers SVM Tracking

For tracking of SVM results (if False Positive, False Neg etc) a tool was created: http://XXXXXXXXX.caltech.edu/~postgres/cgi-bin/svm_results.cgi This web-based tool will automatically track papers that are positive based on our RNAi curation pipeline/checkout form and the OA; That is if a paper is on the checkout form and is curated, the data will be in the OA and marked as a True Positive. If the paper on the checkout list is a False Positive, the curator must note this on the paper editor (Flag False Positive) and the results will be forwarded to the SVM tracking form. http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi The SVM lows that do contain RNAi data are added to the checkout form by a curator (see above) and will be dealt with as any other paper on the list. The SVM lows that actually do not contain RNAi data must be entered manually onto the SVM tracking form as False Positives. To do this go to http://XXXXXXXXX.caltech.edu/~postgres/cgi-bin/svm_results.cgi Under "Enter Curator Results" Select data type/ select curator negative / add the list of negatives to / select comment "SVM positive - Curator negative"

RNAi OA Postgres Tables (rna_*)

CG updated 9-1-2015

postgres tables
rna_anatomy	rna_goprocess	rna_person_hst
rna_anatomyquality	rna_goprocessquality	rna_phenotype
rna_child_of	rna_heatsens	rna_phenotype_hst
rna_child_of_hst	rna_heatsens_hst	rna_phenotypenot
rna_coldsens	rna_historyname	rna_phenotypenot_hst
rna_coldsens_hst	rna_historyname_hst	rna_phenremark
rna_curator	rna_laboratory	rna_phenremark_hst
rna_curator_hst	rna_laboratory_hst	rna_quantdesc
rna_database	rna_lifestage	rna_quantdesc_hst
rna_database_hst	rna_lifestage_hst	rna_quantfromto
rna_date	rna_lifestagequality	rna_quantfromto_hst
rna_date_hst	rna_molaffected	rna_remark
rna_deliverymethod	rna_molaffectedquality	rna_remark_hst
rna_deliverymethod_hst	rna_molecule	rna_sequence
rna_dnatext	rna_molecule_hst	rna_sequence_hst
rna_dnatext_hst	rna_movie	rna_species
rna_exprprofile	rna_movie_hst	rna_species_hst
rna_exprprofile_hst	rna_name	rna_strain
rna_flaggenereg	rna_name_hst	rna_strain_hst
rna_flaggenereg_hst	rna_nodump	rna_suggested
rna_flaggeneticintxn	rna_nodump_hst	rna_suggested_definition
rna_flaggeneticintxn_hst	rna_paper	rna_suggested_definition_hst
rna_fromgenereg	rna_paper_hst	rna_suggested_hst
rna_fromgenereg_hst	rna_pcrproduct	rna_temperature
rna_genotype	rna_pcrproduct_hst	rna_temperature_hst
rna_genotype_hst	rna_penetrance	rna_treatment
rna_gocomponent	rna_penetrance_hst	rna_treatment_hst
rna_gocomponentquality	rna_penfromto
rna_gofunction	rna_penfromto_hst
rna_gofunctionquality	rna_person

RNAi OA

CG updated 9-1-2015

NOTE: Warning: RNAi objects may have multiple lines in the OA due to the nested phenotype data (Penetrance info, etc.)

Dependency Notice: The Community Phenotype Form and the RNAi OA each have separate code to look up the most recent RNAi ID and generate new RNAi IDs based on that. If the code is changed for one, we should also check that the code is changed for the other.

TAB 1

pgid - the postgres ID - NOT DUMPED
Name - rna_name - RNAi : - WBRNAiID #Note: This is automatically assigned
Paper - rna_paper - Reference - ?Paper (Ontology)
Curator - rna_curator - NOT DUMPED - Curator (Dropdown)
PCR Product - rna_pcrproduct - PCR_product - ?PCR_product (Multi-ontology) #Note: EBI/Hinxton will map these
DNA Text - rna_dnatext - DNA_text - Big text #Note: multiple Sequences should be separated by pipe "|" (caution: pressing <ENTER> may cause problems)
Strain - rna_strain - Strain - ?Strain (Ontology)
Genotype - rna_genotype - Genotype - Big text
Treatment - rna_treatment - Treatment - Big text
Temperature - rna_temperature - Temperature - Text (Integer)
Delivery Method - rna_deliverymethod - Delivered_by - (Multi-dropdown) four choices: "Bacterial_feeding", "Injection", "Soaking", "Transgene_expression"
Species - rna_species - Species - ?Species (Dropdown)
Remark - rna_remark - Remark - Big text
Phenotype Observed - rna_phenotype - Phenotype - ?Phenotype ID & name (Multi-ontology)
NOT - rna_phenotypenot - Phenotype_not_observed - NOT Toggle
Phenotype Remark - rna_phenremark - (in-line with Phenotype) Remark - (Big Text)

TAB 2

Phenotype Observed - rna_phenotype - Phenotype - ?Phenotype ID & name (Multi-ontology)
NOT - rna_phenotypenot - Phenotype_not_observed - NOT Toggle
Phenotype Remark - rna_phenremark - (in-line with Phenotype) Remark - (Big Text)
Phenotype Suggestion - rna_suggested - not dumped - field to suggest new phenotype term. Will replace whatever term(s) are currently in the Phenotype field once it is approved
Suggested Definition - rna_suggested_definition - NOT DUMPED - Big text field with definition of new suggested phenotype term
Child Of - rna_child_of - NOT DUMPED - list of parent phenotype term(s) for suggested phenotype
Affected By Molecule - rna_molecule - (in-line with Phenotype) Molecule - ?Molecule (Multi-ontology)
Penetrance From To - rna_penfromto - (in-line with Phenotype) Range - Text (Integer-space-Integer)
Penetrance - rna_penetrance - (in-line with Phenotype) Penetrance - dropdown like in phenotype OA
Quantity From To - rna_quantfromto - (in-line with Phenotype) Quantity - Text (Integer-space-Integer)
Quantity Description - rna_quantdesc - (in-line with Phenotype) Quantity_description - Big text
Heat Sensitive - rna_heatsens - (in-line with Phenotype) Temperature_sensitive - Toggle
Cold Sensitive - rna_coldsens - (in-line with Phenotype) Temperature_sensitive - Toggle

TAB 3

Phenotype Observed - rna_phenotype - Phenotype - ?Phenotype ID & name (Multi-ontology)
NOT - rna_phenotypenot - Phenotype_not_observed - NOT Toggle
Phenotype Remark - rna_phenremark - (in-line with Phenotype) Remark - (Big Text)
Anatomy - rna_anatomy (Multi-ontology)
Anatomy Quality - rna_anatomyquality (Multi-ontology)
Life Stage - rna_lifestage - Life_stage - ?Life_stage (Multi-ontology)
Life Stage Quality - rna_lifestagequality (Multi-ontology)
Molecule Affected - rna_molaffected (Multi-ontology)
Mol Aff Quality - rna_molaffectedquality (Multi-ontology)
GO Process - rna_goprocess (Multi-ontology)
GO P Quality - rna_goprocessquality (Multi-ontology)
GO Function - rna_gofunction (Multi-ontology)
GO F Quality - rna_gofunctionquality (Multi-ontology)
GO Component - rna_gocomponent (Multi-ontology)
GO C Quality - rna_gocomponentquality (Multi-ontology)

TAB 4

Phenotype Observed - rna_phenotype - Phenotype - ?Phenotype ID & name (Multi-ontology)
NOT - rna_phenotypenot - Phenotype_not_observed - NOT Toggle
Phenotype Remark - rna_phenremark - (in-line with Phenotype) Remark - (Big Text)
NO DUMP - rna_nodump - NOT DUMPED - toggle - Prevents data from that row from being dumped. This will also indicate to the Curation Status Form (CSF) that the paper has not been curated and will come up as "oa_blank" in the CSF
From Genereg - rna_fromgenereg - NOT DUMPED - Toggle
Flag Gene Reg - rna_flaggenereg - NOT DUMPED - Toggle
Flag Genetic Intxn - rna_flaggeneticintxn - NOT DUMPED - Toggle
Person Evidence - rna_person - Evidence Person_evidence - multiontology - for ?RNAi object's #Evidence
History Name - rna_historyname - History_name - Text #Note: this field is to accommodate older RNAi objects
Movie - rna_movie - Movie - bigtext #Note: this field is to accommodate older RNAi objects; Note: Separate multiple movie entries with bars (|)
Database - rna_database - Database - Text #Note: this field is to accommodate older RNAi objects; Enter data in this format, split multiple database lines with pipes if there are any :
- Phenobank2 Gene&RNAID GeneID=507328 | Phenobank3 Gene&RNAID GeneID=123456
Expression Profile - rna_exprprofile - Expr_profile - Text #Note: this field is to accommodate older RNAi objects

NOTES ON SUGGESTING NEW PHENOTYPE TERMS THROUGH THE RNAI OA

When suggesting a new phenotype term in TAB 2 of the RNAi OA, curators should make sure to create a PGID/Row with a single placeholder phenotype that is intended to be replaced by the new phenotype term once the new term has been approved
If the data is dumped from the OA for upload before the new term has been approved, the object will dump with the placeholder phenotype term for that upload
This behavior is similar to that of the Phenotype OA
The data entered into the three fields "Phenotype Suggestion", "Suggested Definition", and/or "Child Of" will immediately be populated into the corresponding fields in the New Objects CGI
Cron job:

0 3 * * sun /home/acedb/gary/phn_suggested/phn_suggested_oa.pl

Runs every Sunday at 3 am, checking for entries in rna_suggested (and app_suggested) within the last 7 days and sends Gary S. an e-mail if there are any new entries. If there aren't any, there is no email.

NOT USING

Evidence - postgres table and field not created, don't know what to parse into this field - Text #Note: this field is to accommodate older RNAi objects So there are only 8 RNAi objects that use the Evidence field, and they do so with 'Person_evidence'. In the OA, I think we should include: Person_evidence, Author_evidence, Curator_confirmed, Laboratory_evidence -- C We're only keeping Person_evidence for the #Evidence hash associated with the whole ?RNAi object -- C+J
Penetrance Incomplete - rna_penincomplete - Toggle I think we talked about this, but in case we didn't phenotype OA uses a dropdown for the 4 penetrance types instead of separate toggle fields -- J OK, this sounds like a good idea. Let's just make it a dropdown list here as well -- C
Penetrance Low - rna_penlow - Toggle
Penetrance High - rna_penhigh - Toggle
Penetrance Complete - rna_pencomplete - Toggle
Method - rna_method - Method - Text

Notes

Fields for the tags "Predicted_gene", "Gene", "Transcript", "Pseudogene", "Homol_homol" and "Uniquely_mapped" will be omitted from the OA and populated in ACEDB after probe mapping to the genome at the EBI during the build process.

*.ACE Dumper Documentation

Each RNAi object will need to get dumped with "RNAi" in the "Method" tag

On tazendra, perl module is /home/postgres/work/citace_upload/rnai/get_rnai_ace.pm

Run with script /home/postgres/work/citace_upload/rnai/use_package.pl

Generates rnai.ace.<date> and err.out.<date> (to the day, so it will overwrite previous dumps from the same date) please check dumper and .ace file dumped -- J The dumper seems to be working OK since the dumped *.ACE file you generated is reading in OK, except for the "Evidence" line, as I comment about above in the "Tab3" section. The line currently dumps out as "Person_evidence ..." and it needs to dump out as "Evidence Person_evidence ...", otherwise the file throws errors when reading into ACEDB -- C Fixed, I thought only the innermost tag mattered, but I guess because there's no data in the RNAi part, just the tag, it needs to be there before the #Evidence part -- J I believe so, yes. -- C

Use_package.pl line comments:

'my $outfile = 'rnai.ace.' . $date;' 'my $errfile = 'err.out.' . $date;'

These lines (above) specify the output; change as necessary.

'my ($all_entry, $long_text, $err_text) = &getRnai('all');'

'# my ($all_entry, $long_text, $err_text) = &getRnai('WBRNAi00008227');'

The lines above specify what to dump out of the OA. 'all' dumps everything. If you want to dump specific objects, comment out the top line (add a '#') and uncomment the bottom line (remove '#') and specify the object name where 'WBRNAi00008227' is. Because of permissions, the script will need to be copied, modified, and then run from a permissible directory.

Molecule now converts the pgid stored in postgres with the molecule name in mop_name for that pgid -- J

Error Checks During Dump Process

The following is a list of checks that the .ACE dumper script will perform on all RNAi objects being dumped out of the OA to make sure that the data is consistent and doesn't have any nonsensical information. Any errors that are found will be printed to an "err" file. Every line of the file will list an error message of the general format:

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

where "Dump_status" could be "nodump" (for objects that have a 'fatal' error and will not be dumped) or "flagonly" (for objects that have a 'non-fatal' error and will be dumped).

Fatal Errors (RNAi objects will not get dumped)

1) If there is no identifying RNAi probe information (i.e. the sequence or clone used to knockdown the target gene) in an RNAi object, the dumper script will generate an error message that is printed to the ERROR output file and the object will not get dumped. This is determined by checking that:

a) There is at least one "PCR Product" entry OR

b) There is at least one "DNA Text" entry OR

c) There is at least one "Sequence" entry

If none of these conditions hold true, then an error message will be printed in tab-delimited format like this:

12345   nodump    WBPerson1234   There is no sequence, neither pcrproduct nor dnatext nor sequence

2) If there is no reference (Paper or Person) then the object will not get dumped and an error message is printed:

12345   nodump    WBPerson1234   There is no reference, neither paper nor person

3) If there is no "Phenotype" specified by the curator, the object will not get dumped and an error message will print to the ERROR output file like this:

12345   nodump    WBPerson1234   There is no phenotype

4) If there is no RNAi ID, the object will not get dumped and an error message will print to the ERROR output file like this:

12345   nodump    WBPerson1234   There is no RNAi ID

Non-Fatal Errors (RNAi objects will get dumped, but error message will get printed)

1) If there is no dsRNA "Delivery Method" that has been specified by the curator, the RNAi object will get dumped to the .ACE file, but an error message will print to the ERROR output file like this:

12345   flagonly    WBPerson1234   There is no deliverymethod

2) If there is no "Species" specified by the curator, the RNAi object will get dumped to the .ACE file, but an error message will print to the ERROR output file like this:

12345   flagonly   WBPerson1234   There is no species

3) If no curator is listed for the RNAi object, the RNAi object will get dumped, but an error message will print to the ERROR output file like this:

12345   flagonly   no curator   has no curator