In patzaw/TKCat: Tailored Knowledge Catalog

---

class: code-marg-5

Collections and collection members

ClinVar: Landrum et al. (2018) | TKCat user guide > Collection members | TKCat user guide > Collections

.pull-left[

clinvar <- read_fileMDB(system.file(
   "examples/ClinVar", package="TKCat"
))

clinvar <- read_fileMDB(system.file("examples/ClinVar", package="TKCat"))

pp <- data_model(clinvar) %>%
   plot() %>%
   visOptions(width="100%", height="260px")
pp$sizingPolicy <- htmlwidgets::sizingPolicy(
   browser.defaultWidth = "500px",
   browser.defaultHeight = "260px",
   browser.padding=0,
   browser.fill = FALSE
)
cvif <- hwIframe(
   p=pp,
   style="height:270px; width:100%; border-style:none; background-color:transparent;"
)
cat(cvif)

]

.pull-right[

pp <- data_model(hpo) %>%
   plot() %>%
   visOptions(width="100%", height="100px")
pp$sizingPolicy <- htmlwidgets::sizingPolicy(
   browser.defaultWidth = "500px",
   browser.defaultHeight = "100px",
   browser.padding=0,
   browser.fill = FALSE
)
hpif <- hwIframe(
   p=pp,
   style="height:120px; width:100%; border-style:none; background-color:transparent;"
)
cat(hpif)

]

???

cat(notes$collections)

---

class: code-marg-5 count: false

Collections and collection members

ClinVar: Landrum et al. (2018) | TKCat user guide > Collection members | TKCat user guide > Collections

.pull-left[

clinvar <- read_fileMDB(system.file(
   "examples/ClinVar", package="TKCat"
))

clinvar <- read_fileMDB(system.file("examples/ClinVar", package="TKCat"))

cat(cvif)

]

.pull-right[

cat(hpif)

hpo <- hpo %>% add_collection_member(
   collection="Condition",
   table="HPO_diseases",
   condition=list(
      value="Disease", static=TRUE
   ),
   source=list(
      value="db", static=FALSE
   ),
   identifier=list(
      value="id", static=FALSE
   )
)

]

???

cat(notes$collections)

---

class: code-marg-5 count: false

Collections and collection members

ClinVar: Landrum et al. (2018) | TKCat user guide > Collection members | TKCat user guide > Collections

.pull-left[

clinvar <- read_fileMDB(system.file(
   "examples/ClinVar", package="TKCat"
))

clinvar <- read_fileMDB(system.file("examples/ClinVar", package="TKCat"))

cat(cvif)

collection_members(clinvar)

]

.pull-right[

cat(hpif)

hpo <- hpo %>% add_collection_member(
   collection="Condition",
   table="HPO_diseases",
   condition=list(
      value="Disease", static=TRUE
   ),
   source=list(
      value="db", static=FALSE
   ),
   identifier=list(
      value="id", static=FALSE
   )
)

]

???

cat(notes$collections)

---

class: code-marg-5

Merging with collections

BED: a Biological Entity Dictionary | DODO: Dictionary Of Disease Ontologies | TKCat user guide > Merging with collections

.pull-left[ wzxhzdk:18 ]

???

cat(notes$merging)

---

class: code-marg-5 count: false

Merging with collections

BED: a Biological Entity Dictionary | DODO: Dictionary Of Disease Ontologies | TKCat user guide > Merging with collections

.pull-left[ wzxhzdk:20 wzxhzdk:21 ] .pull-right[ wzxhzdk:22 wzxhzdk:23 ]

???

cat(notes$merging)

patzaw/TKCat documentation built on June 12, 2025, 11:04 a.m.