Pattern documentation

[cmungall]

Manually authored README:

https://github.com/monarch-initiative/mondo/blob/master/src/patterns/README.md

• [x] all links are broken

Auto-generated docs, all in one page:

https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/README.md

• [x] IRIs are broken
• [x] link to TSVs are broken
• [ ] many say This is auto-generated. Add your description here @nicolevasilevsky can you make nice text
• [ ] some say things like Variables | owl_thing (owl:Thing) which is not good
• [ ] these should be integrated with main mondo docs
• [ ] variable names should be meaningful. Stuff that came from patternizer may have variable names like v0

[cmungall]

It would be awesome if in addition to a link to a head foo.tsv | tbl2ghwiki to make a sample table

#!/usr/bin/perl

my $n=0;
my $len;
my $hlen;
while(<>) {
    chomp;
    if ($n==0 && m@^\#@) {
        s@^\#@@;
    }
    my (@vals) = split(/\t/,$_);
    @vals = map {s@\|@, @g; $_} @vals;
    if (!$hlen) {
        $hlen = scalar(@vals);
    }
    while (scalar(@vals) < $hlen) {
        push(@vals, '');
    }
    print '|'.join('|',@vals)."|\n";
    $nulen = scalar(@vals);
    if ($n > 0) {
        if ($len ne $nulen) {
            print STDERR "MISMATCH: $len != $nulen\n";
        }
    }
    $len = $nulen;
    if ($n ==0) {
        @vals = map {"---"} @vals;
        print '|'.join('|',@vals)."|\n";
    }
    $n++;
}

[matentzn]

I have updated the pages:

• all links and IRIs fixed
• Data preview tables added with links to the whole tables.

The rest would have to be done by curating the patterns themselves. @cmungall can you check that, aside from the content, this looks ok to you: https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/README.md

[matentzn]

(I am using python for the generation of this table, pandas has a nice .to_markdown() function.)

[cmungall]

(I am using python for the generation of this table, pandas has a nice .to_markdown() function.)

much better than my hack, awesome. pandas + dosdp-query is a powerful combo!

[cmungall]

@nicolevasilevsky when curating patterns take a look at the patternizer output to see if there is useful stuff to add

E.g.

https://github.com/cmungall/owl_patternizer/blob/master/examples/mondo/X_has_modifier_has_an_isolated_presentation.yaml#L38-L43

looks like a good synonym pattern for isolated!

See https://github.com/monarch-initiative/mondo/pull/2162/files

[cmungall]

the new markdown is looking great

I don't think the vars field is correct https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/README.md#isolated

it should say disease (owl:Thing) based on:

classes:
    isolated: MONDO:0021128

    owl_thing: owl:Thing
relations:
    has modifier: RO:0002573

vars:
    disease: owl_thing

of course, we should just change the range to the root of mondo here, we obviously don't want to allow this to be any thing

The patternizer actually does a good job here, I recommend using it:

https://github.com/cmungall/owl_patternizer/blob/master/examples/mondo/X_has_modifier_has_an_isolated_presentation.yaml#L11

[matentzn]

Are you sure that is how you want the variable slot to be rendered? Just check the second example you posted (https://github.com/cmungall/owl_patternizer/blob/master/examples/mondo/X_has_modifier_has_an_isolated_presentation.yaml#L11). IN this case, the overview would read: v0 (MONDO:0000001). Anyways, I will do this now, but better double-check this is what you want.

[cmungall]

of course we should rename v0 to something meaningful

On Tue, Oct 20, 2020 at 2:55 AM Nico Matentzoglu notifications@github.com wrote:

Are you sure that is how you want the variable slot to be rendered? Just check the second example you posted ( https://github.com/cmungall/owl_patternizer/blob/master/examples/mondo/X_has_modifier_has_an_isolated_presentation.yaml#L11). IN this case, the overview would read: v0 (MONDO:0000001). Anyways, I will do this now, but better double-check this is what you want.

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[nicolevasilevsky]

Reassigning this to @sabrinatoro, I don't have the bandwidth to work on this.