Dear CAFA4 team, We try to use one keyword "convolutional neural network" listed in https://www.biofunctionprediction.org/cafa-targets/keywords.txt but the check format program report it is an illegal keyword. After digging the cafa4_format_check.py, it seems only to accept the following keywords which are not consistent with the one in the above link. legal_keywords = [ "sequence alignment", "sequence-profile alignment", "profile-profile alignment", "phylogeny", "sequence properties", "physicochemical properties", "predicted properties", "protein interactions", "gene expression", "mass spectrometry", "genetic interactions", "protein structure", "literature", "genomic context", "synteny", "structure alignment", "comparative model", "predicted protein structure", "de novo prediction", "machine learning", "genome environment", "operon", "ortholog", "paralog", "homolog", "hidden Markov model", "clinical data", "genetic data", "natural language processing", "other functional information" ] Which one should we follow? Regards, Jia-Ming

Created by Jia-Ming Chang warnname
Did the submissions get reevaluated? Mine still says INVALIDATED and I have not received any additional emails.
Submissions will be automatically get reevaluated (this process has started). If you were able to validate your submission locally using the code from github, you should not need to resubmit. I apologize for the inconvenience. -Scott
We are getting similar errors about keywords from the server, but everything passes locally with the latest version of the checker (git sha a1a0e68e). Will all invalidated submissions be reevaluated automatically, or should we reupload to trigger a new evaluation?
Jia-Ming, I apologize for the problem. We're looking into it and will let you know when it is fixed.
Dear Tim, Ya, our submission is still invalid where we got a quite rare error message: ``` submission name: NCCUCSIIS.zip submission ID: 9699102 ERROR: 'bool' object is not iterable ``` However, local format checking shows our file is correct. ``` warnname@jmchang-MacBookPro cafa-format-check-cafa4 % ./cafa4_format_checker.py ~/GoogleDrive/Google_proj/202001_CAFA4/results/submit/NCCUCS.zip ******************** TESTING /Users/warnname/GoogleDrive/Google_proj/202001_CAFA4/results/submit/NCCUCS.zip VALIDATION SUCCESSFUL NCCUCS.zip meets CAFA4 file naming specifications ``` Any suggestions about the error message? Regards, Jia-Ming
Hi @warnname, I updated the validation script (I made sure the right branch was pulled) and re-ran your submissions. Did you get an email about the latest run? It looks like that submission is still invalid. Tim
Thanks for updating https://github.com/idoerg/cafa-format-check. I am wondering whether the format checker included the submission pipeline is updated or not since we received the following error message after submitting our prediction. --- submission name: NCCUCS.zip submission ID: 9699036 ERROR: Error in NCCUCS_3_287_go.txt, line 3, KEYWORDS: **illegal keyword convolutional neural network** ----- Regards, Jia-Ming
Hi @warnname, Thank you for bringing this our attention. We have made the updates to the [Github repo](https://github.com/idoerg/cafa-format-check) as well as the validation pipeline. Thank you, Tim
The list of keywords at https://www.biofunctionprediction.org/cafa-targets/keywords.txt is correct and the check format program is incorrect. We will update the format checker repo on github soon and update this thread when the update is available. Thanks.

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