Extracting table data from library

[VECorwin]

How would someone extract the schema specific data needed in order to populate lists of all of the possible values for the pathological, and clinical values for the T, N, M, and Stage Group fields? So that these values can be used to populate application drop-down selection boxes.

Does the TNM library contain such listings, and if so, would they cover the DX years before 2018, after, or both? If the values are available, and cover all years are there any special instructions in order to differentiate between the various DX years (before/after 2018)? If the TNM library only covers one of the 2 time span, is there another library from which we can extract the other set of values (either TNM - DX prior to 2018, or AJCC TNM - DX 2018+)?

[ctmay4]

As for the first part of your question, the library completely supports populating lists and we do it in many projects. For example, in SEER*RSA, here is a list of values for Clinical T Appendix.

https://staging.seer.cancer.gov/tnm/input/1.9/appendix/clin_t

The steps are:

• Find a schema. Use either schema lookup or get by ID if you know the schema you are interested in.
• Use StagingSchema.getInputs()' to get all the inputs. Find clin_t by key (input.getKey())or NAACCR item number (input.getNaaccrItem()`)
• StagingSchemaInput.getTable() will return the table identifier to a table which has all the values.
• Get the table using Staging.getTable(id) with the table identifier from the previous step.
• Access the rows to build your lookup.

Here is a basic example:

Staging staging = Staging.getInstance(TnmDataProvider.getInstance(TnmDataProvider.TnmVersion.LATEST));

List<StagingSchema> lookup = staging.lookupSchema(new TnmSchemaLookup("C629", "9231"));
assertEquals(1, lookup.size());
assertEquals("testis", lookup.get(0).getId());

StagingSchema schema = lookup.get(0);

// find "clin_t" in the list of inputs
StagingSchemaInput input = schema.getInputs().stream().filter(x -> x.getKey().equals("clin_t")).findFirst().orElse(null);
assertNotNull(input);

StagingTable table = staging.getTable(input.getTable());
assertNotNull(table);

// I'm just dumping the headers and values here; you can look at the column definitions to determine
// the types of columns to see how you want to display them; I am converting newlines to "\n" to make
// it more readable here, but you probably wouldn't do that.
System.out.println(table.getColumnDefinitions().stream().map(StagingColumnDefinition::getName).collect(Collectors.joining(",")));
table.getRawRows().forEach(x -> System.out.println(String.join(",", x).replace("\n", "\\n")));

Outputs:

Clinical T,Clinical T Display,Description,Registrar Notes
cX,cTX,Primary tumor cannot be assessed,Clinical classification criteria met, evaluation done: \n    Physician unable to assess T \n    Extension cannot be determined\nPhysician assigns cTX, no other information available to determine T
c4,cT4,Tumor invades scrotum \nWITH or WITHOUT vascular lymphatic invasion*#,Dartos muscle, ipsilateral\nScrotum, ipsilateral\n\nExtension to scrotum, contralateral\nUlceration of scrotum\n\nPenis\n\nFurther contiguous extension\n\nStated as T4
88,88,Not applicable,Primary site/histology not TNM defined\nDeath certificate only (DCO) case
,BLANK,See Registrar Notes,Clinical classification criteria not met \nClinical classification criteria met, evaluation done:\n    No information about diagnostic workup\n    Results not documented in record\nClinical evaluation of primary tumor not done or unknown if done\nTumor first detected on surgical resection (no clinical workup)\nEvidence of metastatic disease [(cM1) or (pM1)], no other workup\nOnly Clinical Stage Group documented (no T, N, or M information available)

For the second part of the question I'm not sure about the year ranges. @schusslern could you please comment?

[schusslern]

TNM covers the UICC 7th enhanced values for T, N, M and Stage Group for 2016-2017 as used by the SEER program. There are a few differences between this and the AJCC 7th, which we did try to note clearly in the tables. Since this is 7th edition based, it could be used for any year 7th edition was used, but as I mention, it is not strict AJCC codes.
TNM also includes the Site Specific Factors related to each schema.

EOD would be used for 2018 and later, but does not contain AJCC 8th edition values.
In addition to the EOD Primary Tumor, EOD Regional Nodes, EOD Mets and Summary Stage 2018, it includes the Site Specific Data Items and Grade Clin, Path and Post Therapy related to each schema.

If you need strict AJCC lookups (7th or 8th), you would have to contact the AJCC for licensing.

[VECorwin]

So, correct me if I'm misunderstanding, but I think you're saying that none of the IMS libraries cover the AJCC 8th edition TNM codes that are part of the NAACCR layout with field numbers ranging from 1001 to 1040 and all having names that start with the "AJCC TNM..." prefix, correct? Yes I know that these fields are only valid for cases diagnosed in 2018 or beyond.

[schusslern]

sadly that is correct - you would need to contact AJCC for their API