Data Jamboree 1/Annotation Experiment

From phenoscape
Jump to: navigation, search

Background and Participant Preparation

An annotation experiment was conducted on day 2 of the April 2008 Data Jamboree in order to assess curation consistency among the four trained participants. Training consisted of a hands-on group annotation exercise on day 1, and individual work on each participant's own publications with assistance from project personnel on days 1 and 2. An Annotation Guide with examples of character types commonly encountered in the fish systematic literature was also given to participants. For the experiment, participants were given 2 hours to annotate 10 characters (plus one extra credit) taken from three publications.

Results and Conclusions

Completeness of annotations

Three of the four participants attempted annotations for all 11 characters, while one participant finished only 7 characters. All participants recorded the character number and textual description, and selected the appropriate voucher specimen for each annotation. Only two of the four participants recorded evidence codes for each annotation.

Variability of EQ statements

A summary of annotation consistency among participants is presented in the table below (incomplete annotations due to software issues are excluded).

Character # # Participants with

Completed Annotations*

 % Consistency with Key Variable component of annotation
1 4 100
2 3 0 post-composition of Q term for relative length
3 3 0 incorrect recording of count values
4 4 0 TAO term definition confusion (bone vs. cartilage)
5 3 33 E post-composition; choice of appropriate Q
6 4 0 E post-composition
7 4 50 E post-composition
8 3 33 choice of appropriate Q term
9 3 0 E post-composition; choice of appropriate Q term
10 2 50 choice of appropriate Q term
EC 2 25 E post-composition; choice of appropriate Q term
    • incomplete annotations due to software issues were excluded

Participants annotated only one character identically. Variation in other annotations was due to several reasons:

  • Granularity of annotations. Some participants integrated very detailed information in post-compositions of entities or qualities, whereas others used single anatomy terms or broad term categories for quality. Use of spatial information in post-composition also varied among participants.
  • Creation of post-composed entities. Participants had difficulty in deciding what term to use as the genus in post-composition. Also, the relation used in post-composition (for example, use of part_of/has_part) differed in annotations among participants.
  • Choice of the appropriate quality term. Participants had difficulty in choosing quality terms among many similar choices. The appropriate use of monadic and relational qualities also differed in the annotations among participants.
  • Confusion regarding the definition of ontology terms. For one character, confusion about the identity of a term resulted in differing annotations, and points to the need for consistent term names for bones in the TAO.

The results of the annotation experiment provide detailed areas for improvement in establishing curation standards to assist in annotation, and stream-lining of the software interface so that curators are not faced with similar and inapplicable choices for terms and relations. Based on these results, curation standards and improvement to the Annotation Guide are in development, and improvements to the Phenote interface are planned.

Instructions to Participants

In the following exercise, we would like to assess annotation consistency among data jamboree participants working independently on a common set of characters. These characters are taken directly from the literature of comparative morphology of fishes.

Download the annotation-experiment folder from the Phenoscape server.

Use the taxon list and the character matrix given in Table 1 to annotate characters 1-11 below. For the purpose of this exercise, character states noted in Table 1 were observed in all specimens listed in the materials list. The name of this publication is: Lapp and Dahdul, 2008.

Table 1. Character matrix
Taxon 1 2 3 4 5
6
7
8
9
10
EC
Chanos chanos 0 0 0 0 0 0 0 0 0 0 0
Diplomystes chilensis 0 0 0 1 0 0 0 0 0 1 0
Hiodon alosoides 1 1 1 2 1 1 1 1 1 2 1

1. Presence or absence of intercalar: (0) present; (1) absent.

2. Opercle depth to width ratio: (0) less than two; (1) about two or greater than two. Essentially, this character distinguishes between those taxa with a short, relatively broad opercle and those with a tall relatively slender opercle.

3. Number of unbranched plus branched pelvic-fin rays: (0) 11; (1) nine; (2) more than 11.

4. Basihyal: (0) present and ossified; (1) present and cartilaginous; (2) absent.

5. Position of anterior margin of nasal: (0) falling short of lateral process of mesethmoid (= lateral ethmoid wing of Weitzman, 1962); (1) extending anteriorly to overlie or extend beyond lateral process of mesethmoid.

6. Number of hypurals in upper lobe of caudal fin: (0) four; (1) three.

7. Presence or absence of medially directed, spine-like process on ventral surface of post-temporal: (0) present; (1) absent.

8. Presence or absence of contact between frontal and pterotic: (0) frontal and pterotic bones in contact; (1) pterotic excluded from contact with frontal by sphenotic.

9. Orientation of infrapharyngobranchial 1: (0) proximal tip anteriorly directed; (1) proximal tip posteriorly directed.

10. Infraorbital 6: (0) triangular; (1) triradiate; (2) tubular.

Extra Credit: Form of parasphenoid: (0) relatively straight anteroposteriorly and with posterior portion of bone aligned approximately along longitudinal axis of anterior portion of vertebral column; (1) with distinct anteroposterior curvature and with posterior portion of bone located distinctly ventral to longitudinal axis through anterior portion of vertebral column. (Zanata & Vari, 2005)

References
  • Hilton, EJ. 2003. Comparative osteology and phylogenetic systematics of fossil and living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha). Zoological Journal of the Linnean Society 137:1-100.
  • Sanger, TJ and AR McCune. 2002. Comparative osteology of the Danio (Cyprinidae: Ostariophysi) axial skeleton with comments on Danio relationships based on molecules and morphology. Zoological Journal of the Linnean Society 135: 529-546.
  • Zanata AM and Vari RP. 2005. The family Alestidae (Ostariophysi, Characiformes): a phylogenetic analysis of a trans-Atlantic clade. Zoological Journal of the Linnean Society 145: 1-144.

Raw Data from Participants

Character Number Character State Participant Entity Name Quality Name Additional Entity Name Count Measurement Unit Name
1 0 key intercalar present
1 0 1 intercalar present
1 0 2 intercalar present
1 0 3 intercalar present
1 0 4 intercalar present
1 1 key intercalar absent
1 1 1 intercalar absent
1 1 2 intercalar absent
1 1 3 intercalar absent
1 1 4 intercalar absent
2 0 key opercle depth^relative_to(width) <2 ratio
2 0 1 opercle depth^relative_to(width) opercle <2 ratio
2 0 2 opercle
2 0 3 opercle increased width decreased height
2 0 4 opercle relational shape quality <2
2 1 key opercle depth^relative_to(width) >, = 2
2 1 1 opercle depth^relative_to(width) >, = 2 ratio
2 1 2 opercle
2 1 3 opercle increased height decreased height
2 1 4 opercle relational shape quality 2 or >
3 0 key pelvic fin lepidotrichium count 11
3 0 1 pelvic fin lepidotrichium count 11
3 0 2 pelvic fin lepidotrichium count 11
3 0 3 pelvic fin lepidotrichium count 11
3 0 4 accessory pretectal nucleus count 11
3 1 key pelvic fin lepidotrichium count 9
3 1 1 pelvic fin lepidotrichium count 9
3 1 2 pelvic fin lepidotrichium count 9
3 1 3 pelvic fin lepidotrichium count 9
3 1 4 pelvic fin count >11
3 1 key pelvic fin count >11
3 2 1 pelvic fin lepidotrichium count 11
3 2 2 pelvic fin lepidotrichium count 11
3 2 3 pelvic fin lepidotrichium count 11
3 2 4 pelvic fin count 11
4 0 key basihyal present
4 0 1 basihyal^is_a(bone) present
4 0 2 basihyal cartilage ossified
4 0 3 basihyal ossified
4 0 4 basihyal ossified
4 1 key basihyal cartilage present
4 1 1 basihyal cartilage present
4 1 2 basihyal cartilage cartilaginous
4 1 3 basihyal cartilaginous
4 1 4 basihyal cartilaginous
4 2 key basihyal cartilage absent
4 2 1 basihyal absent
4 2 2 basihyal cartilage absent
4 2 3 basihyal absent
4 2 4 basihyal absent
5 0 key nasal bone separated from mesethmoid bone
5 0 1 nasal bone^has_boundary(posterior) position mesethmoid bone
5 0 2 anterior margin^part_of(nasal bone) separated from mesethmoid bone
5 0 3 nasal bone length^ends_earlier_than(length) mesethmoid bone^part_of(lateral ethmoid process)
5 0 4 nasal bone posterior to
5 0 4 nasal bone posterior to
5 1 key nasal bone overlaps with lateral ethmoid ventral wing
5 1 1 basihyal composition
5 1 2 anterior margin^part_of(nasal bone) overlap with mesethmoid bone
5 1 3 nasal bone length^ends_during(length) mesethmoid bone^part_of(lateral ethmoid process)
5 1 4 nasal bone lateral to
6 0 key hypural^part_of(caudal fin) count 4
6 0 1 hypural count caudal fin^has_integral_part(caudal fin upper lobe) 4
6 0 2 hypural count caudal fin upper lobe 4
6 0 3 caudal fin upper lobe^contains(hypural) count 4
6 0 4 caudal fin upper lobe^arises_from(medial surface) count 4
6 1 key hypural^part_of(caudal fin) count 3
6 1 1 hypural count caudal fin^has_integral_part(caudal fin upper lobe) 3
6 1 2 hypural count caudal fin upper lobe 3
6 1 3 caudal fin upper lobe^contains(hypural) count 3
6 1 4 caudal fin upper lobe count 3
7 0 key bony projection^part_of(ventral surface)^part_of(posttemporal) present
7 0 1 posttemporal present posttemporal^has_part(specialized hemal arch and spine) 4
7 0 2 bony projection^part_of(ventral surface)^part_of(posttemporal) present
7 0 3 bony projection^contained_in(posttemporal) present
7 0 4 bony projection^part_of(posttemporal) absent
7 0 key bony projection^part_of(ventral surface)^part_of(posttemporal) absent
7 1 1 posttemporal present posttemporal^has_part(specialized hemal arch and spine) 3
7 1 2 bony projection^part_of(ventral surface)^part_of(posttemporal) absent
7 1 3 bony projection^contained_in(posttemporal) absent
7 1 4 bony projection^part_of(posttemporal) present
8 0 key frontal bone in contact with pterotic
8 0 2 frontal bone in contact with pterotic
8 0 3 frontal bone pterotic
8 0 3 frontal bone pterotic
8 0 4 frontal bone pterotic
8 1 key frontal bone separated from pterotic
8 1 2 frontal bone separated from pterotic
8 1 3 frontal bone pterotic
8 1 4 frontal bone pterotic
8 1 4 frontal bone pterotic
9 0 key proximal region^part_of(pharyngobranchial 1 bone) anteriorly rotated
9 0 2 proximal region^part_of(pharyngobranchial 1 bone) anterioralized
9 0 3 pharyngobranchial 1 bone
9 0 4 anatomical region^arises_from(medial surface)^part_of(pharyngobranchial 1 bone) anteriorly rotated
9 1 key proximal region^part_of(pharyngobranchial 1 bone) posteriorly rotated
9 1 2 proximal region^part_of(pharyngobranchial 1 bone) posterioralized
9 1 3 pharyngobranchial 1 bone
9 1 4 anatomical region^arises_from(medial surface)^part_of(pharyngobranchial 1 bone) posteriorly rotated
10 0 key infraorbital 6 triangular
10 0 2 infraorbital 6 triangular
10 0 3 infraorbital 6 shape
10 0 4 infraorbital 4 posteriorly rotated
10 1 key infraorbital 6 tripartite
10 1 2 infraorbital 6 tripartite
10 1 3 infraorbital 6 shape
10 1 4 infraorbital 4 posteriorly rotated
10 2 key infraorbital 6 cylindrical
10 2 2 infraorbital 6 cylindrical
10 2 3 infraorbital 6 shape
10 2 4 infraorbital 4 anteriorly rotated
ECa
0 key anterior/posterior axis^part_of(parasphenoid) straight angle
ECa
0 4 parasphenoid straight angle
ECa
0 2 anterior/posterior axis^part_of(parasphenoid) straight angle
ECa
1 key anterior/posterior axis^part_of(parasphenoid) curved ventral
ECa
1 4 parasphenoid curved ventral
ECa
1 2 anterior/posterior axis^part_of(parasphenoid) curved vertebral column
ECb
0 key posterior region^part_of(parasphenoid) aligned with anterior region^part_of(vertebral column)
ECb
0 2 posterior region^part_of(parasphenoid) aligned with vertebral column
ECb
1 key posterior region^part_of(parasphenoid) ventral to anterior region^part_of(vertebral column)
ECb
1 2 posterior region^part_of(parasphenoid) ventral to