07 May 2022, 16:44
Hi Irene, The issue with the missing taxonomy terms has now been fixed. I've provided a crosswalk for you below to further clarify my earlier comments about how to map the entities from the XML to the entries in the wiki.
AOP 69 now has the following section summarizing the applicability information
<applicability>
<sex>
<evidence>High</evidence>
<sex>Male</sex>
</sex>
<life-stage>
<evidence>High</evidence>
<life-stage>Adult, reproductively mature</life-stage>
</life-stage>
<taxonomy taxonomy-id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a">
<evidence>High</evidence>
</taxonomy>
<taxonomy taxonomy-id="9f3880fe-e513-45a8-8050-fbd010dcbab9">
<evidence>High</evidence>
</taxonomy>
</applicability>
You will see that it now includes two <taxonomy> entries that weren't there before. The identifiers for these entries correspond to the following records that are defined earlier in the XML data structure:
<taxonomy id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a">
<source-id>10116</source-id>
<source>NCBI</source>
<name>Rattus norvegicus</name>
</taxonomy>
<taxonomy id="9f3880fe-e513-45a8-8050-fbd010dcbab9">
<source-id>9606</source-id>
<source>NCBI</source>
<name>Homo sapiens</name>
</taxonomy>
There are also two references at the end of the XML:
<taxonomy-reference id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a" aop-wiki-id="66"/>
<taxonomy-reference id="9f3880fe-e513-45a8-8050-fbd010dcbab9" aop-wiki-id="1"/>
So as you can see, after our most recent update, both the taxonomy domains are consistent between the web interface and the XML. This change is immediate when accessing the dynamic XML for individual AOPs. The examples above are derived from here: https://aopwiki.org/aops/69.xml. The nightly download file (https://aopwiki.org/downloads/aop-wiki-xml.gz) will be correct as of tomorrow (5/8/2022). It will also be corrected in our next quarterly release on July 1, 2022. We do not correct errors in previous permanent downloads.
As noted before, the aop-wiki-id for taxonomy terms is not that useful because we don't expose those identifiers. For AOPs, key events, relationships, and stressors, however, these IDs will reference the specific pages in the wiki. For example, AOP 69 has the following identifier in this version of the XML:
<aop id="f69369fd-e613-4f53-a019-06eb7df29efb">
<aop-reference id="f69369fd-e613-4f53-a019-06eb7df29efb" aop-wiki-id="69"/>
Note that the identifiers used within the XML are regenerated each time the XML is created, so those identifiers cannot be used to compare like entities between one XML file and the next. For that, you will need to use the vendor IDs at the bottom of the XML file. These will remain constant from one download file to the next since they correspond to our internal identifiers in the wiki itself.
Let me know if you have any further questions or notice any additional discrepancies.
AOP 69 now has the following section summarizing the applicability information
<applicability>
<sex>
<evidence>High</evidence>
<sex>Male</sex>
</sex>
<life-stage>
<evidence>High</evidence>
<life-stage>Adult, reproductively mature</life-stage>
</life-stage>
<taxonomy taxonomy-id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a">
<evidence>High</evidence>
</taxonomy>
<taxonomy taxonomy-id="9f3880fe-e513-45a8-8050-fbd010dcbab9">
<evidence>High</evidence>
</taxonomy>
</applicability>
You will see that it now includes two <taxonomy> entries that weren't there before. The identifiers for these entries correspond to the following records that are defined earlier in the XML data structure:
<taxonomy id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a">
<source-id>10116</source-id>
<source>NCBI</source>
<name>Rattus norvegicus</name>
</taxonomy>
<taxonomy id="9f3880fe-e513-45a8-8050-fbd010dcbab9">
<source-id>9606</source-id>
<source>NCBI</source>
<name>Homo sapiens</name>
</taxonomy>
There are also two references at the end of the XML:
<taxonomy-reference id="03a2d35e-5ce7-4275-aabf-65bc0c81f54a" aop-wiki-id="66"/>
<taxonomy-reference id="9f3880fe-e513-45a8-8050-fbd010dcbab9" aop-wiki-id="1"/>
So as you can see, after our most recent update, both the taxonomy domains are consistent between the web interface and the XML. This change is immediate when accessing the dynamic XML for individual AOPs. The examples above are derived from here: https://aopwiki.org/aops/69.xml. The nightly download file (https://aopwiki.org/downloads/aop-wiki-xml.gz) will be correct as of tomorrow (5/8/2022). It will also be corrected in our next quarterly release on July 1, 2022. We do not correct errors in previous permanent downloads.
As noted before, the aop-wiki-id for taxonomy terms is not that useful because we don't expose those identifiers. For AOPs, key events, relationships, and stressors, however, these IDs will reference the specific pages in the wiki. For example, AOP 69 has the following identifier in this version of the XML:
<aop id="f69369fd-e613-4f53-a019-06eb7df29efb">
<aop-reference id="f69369fd-e613-4f53-a019-06eb7df29efb" aop-wiki-id="69"/>
Note that the identifiers used within the XML are regenerated each time the XML is created, so those identifiers cannot be used to compare like entities between one XML file and the next. For that, you will need to use the vendor IDs at the bottom of the XML file. These will remain constant from one download file to the next since they correspond to our internal identifiers in the wiki itself.
Let me know if you have any further questions or notice any additional discrepancies.