AOP Forum - AOP-Wiki Technical Assistance

Pdf attachments

Mon, 20 Jan 2025 09:48:41 +0000

Hello,
Have any of you have problems uploading pdf attachments to your AOP? I have done it previously, but in the recent days the system it is not allowing me to upload PDF files, only image-type files. Any suggestions?

Thank you!

Claudia

Ontology versions in KE Components

Tue, 08 Oct 2024 08:47:39 +0000

Hello,
My colleague and I are trying to work with the ontologies that were used to annotated KEs, specifically under the KEC Biological Process. First going through all GO (gene ontology) terms, we are struggling to find all mappings of GO terms to genes (which is frequently done for gene set enrichment studies). Out of the 600-ish GO terms, we can not find about 10% of the terms using conventional mapping tools (GO package, MSigDb, ...). Manual searching indicates that GO terms might be obsolete and not anymore in the current versions of GO. Is there a way to find out which version of the ontology is used in AOP-Wiki, or whether there are updates to the ontologies used in the AOP-Wiki? For completeness, it would be great if such information can be found in the help page (https://www.aopwiki.org/info_pages/2/inf...ed_pages/7).

Incosistencies between XML and AOP-Wiki displayed content

Wed, 19 Apr 2023 13:30:29 +0000

With the advent of Wiki 2.6 we dusted off a bit our XML parser to make it ready for the new AOP-Wiki features.

We discovered 3 possible inconsistencies and I thought it would be best to report them here.

So here there are:

1) No tag in the XML for "Strategy" subsection (under "AOP Development Strategy" section).

How to reproduce:

Example is AOP 423. Go to https://aopwiki.org/aops/423 and https://aopwiki.org/aops/423.xml Note that while "Context" is listed in the XML unde "/aop/background" the "Strategy" content although visible in the wiki is not found in the XML. Search for "In this stud" to verify.

2) No tag in the XML for "Known Modulating Factors" subsection (under "Overall Assessment of the AOP" section).

3) Duplication of content under "/aop/essentiality-support" and "/aop/overall-assessment/key-event-essentiality-summary".

How to reproduce:

Example is again AOP 405. Go to https://aopwiki.org/aops/405 and https://aopwiki.org/aops/405.xml Search for "AChE is a serine" in both tabs. It will be found one time in the AOP-Wiki display page and 2 times in the XML.

Hopefully these are (will be) fixed for 2.6.

is not always visible in the rendered wiki page

Tue, 05 Apr 2022 13:19:00 +0000

Hi,

We noticed an inconsistency between the latest XML and some key events and maybe you could help us a bit to understand what's going on.

Case in point are events 1043, 1492, 1493 which have a non-empty like Cellular or Tissue but it is not rendered in the wiki page.

In contrast, in the event 1847 that has the exact same value (Cellular) is visible.

https://aopwiki.org/events/1847

There is a screenshot depicting the issue attached.

So why some in some key event is rendered and in some it is not rendered?

Thanks in advance

Vassilis

event-1043-no-biological-context.png (Size: 132.51 KB / Downloads: 1)

Taxonomic applicability TAG discrepancy between AOP, KE AND KER

Tue, 05 Apr 2022 12:47:26 +0000

Hi,

I noticed that the containing tag in KER (as per XSD) is (of appicability-type) while in AOP an KE the tag name is .

In AOPs/KEs

while in KERs

Are these two tags different by design? Can we make them both 'applicability'? so Sex/Life Stage/taxonomy are not listed under taxonomic-applicability in KERs?

Thanks in advance

Vassilis

Taxonomic applicability discrepancy between XML and UI

Wed, 02 Mar 2022 14:32:37 +0000

I am working with your latest released (https://aopwiki.org/downloads/aop-wiki-xml-2022-01-01.gz) dump and I've noticed missing or different information in it when compared to your website.

As an example, the AOP nº 69(https://aopwiki.org/aops/69#taxonomic_applicability) lists to be applicable on rats and humans.
On the XML, this AOP ID only has a taxonomic reference:

""

pointing to rats:
```

    10116
    NCBI
    rats
```

Another example is AOP nº 202(https://aopwiki.org/aops/202#taxonomic_applicability)for which there is no taxonomic reference at all in the XML whereas the webpage says it has humans applicability.

Could you please tell me if I am processing the data in an incorrect way or what is the source of this difference?

Many thanks for your help.
Best,
Irene López

Gardening requests

Wed, 02 Mar 2022 12:26:22 +0000

I have created a new thread for forum users to identify issues for the gardeners to look into:

MySQL error with standard characters

Thu, 24 Jun 2021 05:14:47 +0000

I am trying to add a reference under the 'references' section of the following AOP page: https://aopwiki.org/aops/272 - When in edit mode, if I add the reference as intended:

Rage, E. et al., (2020), "PUMA – pooled uranium miners analysis: cohort profile.", Occup Environ Med. 77:194-200. doi: 10.1136/oemed-2019-105981

I receive the MySQL error. I have tried to diagnose what possible characters in the above cause MySQL trouble (the FAQ mentioned greek letters which is not applicable here). Right now, the change will save if I add the reference as follows:

Rage, E. et al., (2020), "PUMA – pooled uranium miners analysis: cohort profile.", Occup En

But the moment I add the 'v' i.e. '....Occup Env' I begin to receive the error again. I have encountered this issue several times before and resolving it each time is an exercise in trial and error. It is unfortunate and is costing me quite a bit of time each time I have to try and edit the AOP.

Please let me know if I am missing anything.

Best,
Rob.

----------------------------

EDIT 1: I have found the cause of the problem, or at least a potential fix. By removing quotation marks from the publication titles the error disappears. Strange, as many of the references had quotation marks and the AOP saved fine with them. I'm guessing a mixture of quotation ("), double left quotation (“) and double right quotation (”) potentially cause MySQL on the back-end issues by defining potential strings variables erroneously. Perhaps it would be worthwhile to mention this on the FAQ section. The OECD style guidelines specifically ask for quotation marks around titles, see page 59 here: https://www.oecd.org/about/publishing/OE...dition.pdf

EDIT 2: When trying to change the size of the font in the 'references' section for this AOP, I received the MySQL error.

MS Word and AOPWiki

Wed, 03 Mar 2021 16:45:59 +0000

Is anyone interested in a Word template for AOP development. Something that would allow easier tracking of changes when working on teams, use of reference managers etc.

It would mean you will need to cut and paste in to the Wiki to start or update an AOP.

Kevin

Merging KEs

Tue, 16 Feb 2021 15:47:22 +0000

As part of an AOP I am working on, I have identified some potentially synonymous KEs (1521 and 1467). Can these KEs be harmonized and merged? How would I go about that?