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Re: [ontolog-forum] Knowledge graphs by Google and Facebook

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Chris Mungall <cjmungall@xxxxxxx>
Date: Tue, 22 Jan 2013 16:52:43 -0800
Message-id: <ABC5FD4A-75FC-47C4-BE05-A9F5FB1F769E@xxxxxxx>

On Jan 22, 2013, at 9:19 AM, John F Sowa wrote:    (01)

> On 1/22/2013 12:12 PM, Michael Brunnbauer wrote:
>> This Humpty Dumpty word seems to have a lot of use cases....
> 
> Yes, but it is so horribly ambiguous that it makes natural language
> look like the epitome of clarity and precision.
> 
> Recommendation:  There are *always* better solutions than using NULL.
> Don't ever use NULL.    (02)

In 1999 I joined a lab in Berkeley, just as it was embarking on a collaboration 
with Craig Venter's company Celera Genomics to sequence and analyze the genome 
of the fruitfly Drosophila melanogaster.    (03)

The team in charge of building the database were from a mainstream corporate IT 
background, and did not understand the domain. They designed the database 
schema in the fashion they always had, and dutifully declared most of the 
columns NOT NULL.    (04)

The computational biologists in charge of analyzing the genome had to feed 
their results into this database. The biologists understood the domain 
precisely, and knew that some of the data would be incomplete.    (05)

The deadline for the genome analysis was approaching, and the computational 
biologists could not get the IT stafff to change the schema. This was a fairly 
high profile project, with the human genome slated to be next, so the pressure 
was on. When the deadline hit, the database columns were still declared "NOT 
NULL", and the values for many of those colums were still unknown for many 
rows. The biologists had to do something, and so at 2am, after two weeks of 
sleepless hacking and analysis, as desperate as the shoemaker in the Grimm's 
fairytale, they filled all those columns with the string "PRAY FOR ELVES".    (06)

A fly gene was later named "Pray For Elves" in honor:
http://flybase.org/reports/FBrf0151677.html    (07)

I think I still have my old code, which is littered with fragments such as: 
WHERE gene.function != 'PRAY FOR ELVES';    (08)

So, yes, there are better solutions than using NULL. You can always PRAY FOR 
ELVES.    (09)

> 
> John
> 
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