org.dllearner.examples
Class Carcinogenesis

java.lang.Object
  org.dllearner.examples.Carcinogenesis

public class Carcinogenesis
extends Object

This class maps the carcinogenesis Prolog files to an OWL file. In a first step, a Prolog parser is used to read all files. The main step involves applying mapping Prolog clauses to OWL axioms through domain specific mapping rules. The carcinogenesis Prolog files are available here: http://web.comlab.ox.ac.uk/oucl/research/areas/machlearn/cancer.html .f files contain positive and .n files contain negative examples. pte1.n and pte.f contain the PTE-1 challenge examples. train.n and train.f contain other examples which can be used to train for PTE-1. The PTE-2 directory contains PTE-2 files, i.e. all substances referred to in those files are only those of the PTE-2 challenge.

Author:

Jens Lehmann

Constructor Summary

Carcinogenesis()

Method Summary

static String	getPTE2Examples() To find out whether a substance is carinogenetic go to "http://ntp-server.niehs.nih.gov/" and click on "Testing Status of Agents at NTP".
static void	main(String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Carcinogenesis

public Carcinogenesis()

Method Detail

main

public static void main(String[] args)
                 throws FileNotFoundException,
                        IOException,
                        ParseException

Parameters:

args - No arguments supported.

Throws:

IOException

FileNotFoundException

ParseException

getPTE2Examples

public static String getPTE2Examples()

To find out whether a substance is carinogenetic go to "http://ntp-server.niehs.nih.gov/" and click on "Testing Status of Agents at NTP".

Levels:

• CE = clear evidence
• SE = some evidence
• E = equivocal evidence
• NE = no evidence

Levels CE and SE are positive examples. E and NE negative examples. Experiments are performed on rats and mice of both genders, so we have four evidence values. An example is positive if at least one value is SE or CE.

Some values are taken from the IJCAI-97 paper of Muggleton.

Positives (19):

• t3 (SE+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCACAFD4-123F-7908-7B521E4F665EFBD9
• t4 (3CE+NE) - contradicts IJCAI-97 paper and should probably be case 75-52-5 instead of 75-52-8: http://ntp.niehs.nih.gov/index.cfm?objectid=BCE49084-123F-7908-7BE127F7AF1FFBB5
• t5: paper
• t7: paper
• t8: paper
• t9 (3CE+SE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD7C6869-123F-7908-7BDEA4CFAA55CEA8
• t10: paper
• t12 (2SE+E+NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCB0ADE0-123F-7908-7BEC101C7309C4DE
• t14 (2CE+2NE) probably 111-42-2 instead of 11-42-2: http://ntp.niehs.nih.gov/index.cfm?objectid=BCC60FF1-123F-7908-7B2D579AA48DE90C
• t15: paper
• t16 (2CE+SE+E): http://ntp.niehs.nih.gov/index.cfm?objectid=BCC5D9CE-123F-7908-7B959CCE5262468A
• t18 (2SE+E+NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCA087AA-123F-7908-7B79FDFDE3CDCF87
• t19 (2CE+E+NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCAE5690-123F-7908-7B02E35E2BB57694
• t20 (2SE+E+NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCF95607-123F-7908-7B0761D3C515CC12
• t21 (CE+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCFCB63C-123F-7908-7BF910C2783AE9FE
• t22 (SE+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD8345C2-123F-7908-7BC52FEF80F110E1
• t23 (4CE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCADD2D9-123F-7908-7B5C8180FE80B22F
• t24 (CE+E): http://ntp.niehs.nih.gov/index.cfm?objectid=BCFB19FF-123F-7908-7B845E176F13E6E1
• t25 (3CE+SE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD2D2A62-123F-7908-7B0DA824E782754C
• t30 (2CE+SE+E) : http://ntp.niehs.nih.gov/index.cfm?objectid=BCB13734-123F-7908-7BEBA533E35A48B7

Negatives (10):

• t1 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD9FF53C-123F-7908-7B123DAE0A25B122
• t2 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCF8651E-123F-7908-7B21DD5ED83CD0FF
• t4: paper
• t6: paper
• t11: paper
• t13 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD136ED6-123F-7908-7B619EE79F2FD062
• t17: paper
• t26 (2E+2NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD1E6209-123F-7908-7B95EB8BAE662CE7
• t27 (E+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCAC5D00-123F-7908-7BC46ECB72A6C91B
• t28 (E+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD34E02A-123F-7908-7BC6791917B591DF

Unclear (1):

• t29: probably a negative (see http://ntp.niehs.nih.gov/index.cfm?objectid=BD855EA1-123F-7908-7B573FC3C08188DC) but no tests directly for this substance

The following examples are probably not part of the IJCAI PTE-2 challenge (reports younger than 1998):

• pos: t21 (5/99), t25 (9/04), t30(10/01)
• neg: t26 (5/99), t27 (05/01), t28 (05/00), t29 (09/02)

Returns:

A string for all examples as used in the conf file.