User talk:Lbrensk/sandbox

Hi Lbrensk! I think what you have in sandbox is very concise and explains the topic accurately. I study butterflies and have absolutely no background on your topic "Plant Phenology Ontology" or any plant related study, so I am commenting as someone with no knowledge on the topic you chose. Is "Plant Phenology Ontology" considered as a database? - in any case, I feel it is better to explain what PPO is by avoiding jargon. I read your first sentence - "PPO is a collection of OBO Foundry ontologies that facilitate integration of heterogeneous data about plant phenology from various sources" - several times and also briefly read through one of the papers you cited (Stucky et al 2018) and got an idea of what it is, but usually readers of wikipedia are non-scientists, so I think it is important to expand a little bit of your first paragraph and explain a bit more in easy-to-understand words.

Regarding your "General structure" section, those Italicized words (e.g., "measurement datum") confused me a little - I think it is better to explain what they are so that they fit into the paragraph. Your "Recent developments" section also includes these Italicized words. Also, what are those voucher codes (e.g., BCO 0000003) mentioned in this section?

I played around a bit with the Global Plant Phenology Data Portal and apparently people are incorporating data from historical collections (as you mentioned in the third paragraph), is this correct? If yes, I think it is interesting to state that in the "Recent developments" section - I wondered about this when I was reading this section.

Comments from Emily
'''[Nice job, I just have a few comments. Yours is one of the more technical articles, so it would be really helpful if you can add some more sentences here and there to increase its intelligibility for a layperson.]'''

The Plant Phenology Ontology (PPO) is a collection of OBO Foundry ontologies that facilitates integration of heterogeneous data about plant phenology [this should be SEED plants; it does not have information on other lineages, like ferns, etc.] from various sources. These data sources include observations networks, such as the National Ecological Observatory Network (NEON), the National Phenology Network (NPN), and the Pan-European Phenology Database (PEP725), remote sensing, herbarium specimens, and citizen science observations. The initial focus during ontology development was to capture phenological data about one plant or a population of plants as observed by a person, and this enabled integration of data across disparate observation network sources '''[This is rather technical, and I think a layperson would have difficult understanding, from these few sentences, what the PPO is really for. Can you give a broader sentence or two that describes an example of how this information can be used, that will illustrate its purpose more clearly?]'''.

General structure
The structure of the Plant Phenology Ontology relies on integrated terms from other ontologies, notably the Basic Formal Ontology, the Plant Ontology , the Information Artifact Ontology , and the Biological Collections Ontology. The basic structure of the PPO models the 'observing process ' (BCO:0000003), which has an input of a ' whole plant ' (PO:0000003) and an output of a ' measurement datum ' (IAO:0000109). The value of the ' measurement datum ' is determined by what was observed or not observed on the plant. Measurement data in the PPO have upper counts and lower counts for some ' plant structure ' (PO:0009011), and when the upper and lower counts both equal zero, an absence is inferred by the ontology using the HermiT reasoner. Plant Ontology anatomy terms were used to enable the ontology to infer the presence or absence of hierarchical phenological traits using the reasoner. For example, if pollen-releasing flower heads are observed to be present (PPO:0002340) with both upper and lower counts greater than zero, the reasoned ontology can also infer that floral structures are present (PPO:0002026) on the plant '''[Again, something about the ultimate goal here would be helpful... can you extend this example further to say exactly what the input datum might be, and what the output data would be? Some kind of figure illustrating the internal workflow for this example would be extremely helpful!]'''.

Recent developments
Because most observation networks were only established in the early 2000s, they contain a wealth of plant phenological data for the 21st century, but do not offer insight into historical baselines. Herbarium specimens inherently capture the phenological traits of a plant in a specific location at a specific time. Because some herbarium collections date back to the 17th century, herbarium specimens represent an enormous amount of historical phenology data. These data would enable researchers to address new questions about how much the current climate has shifted from historical baselines.

Efforts have been made to expand the scope of the ontology to include observations made on herbarium specimens. Because the backbone of the existing PPO is built around the concept of whole plants, new logic had to be added to enable reasoning over data from parts of plants, because this is usually, though not always, what is captured by an herbarium specimen. The concept of ' portion of a plant ' was added to the ontology, and a new relationship ' is or was part of ' was added to describe how a ' portion of a plant ' relates to a 'whole plant '. The new PPO release allows integration of phenology data from herbarium specimens, provided that observations or phenological scorings for the specimens already exist.

Global Plant Phenology Data Portal
The Global Plant Phenology Data Portal is an interface that allows users to see data that have been ingested by the PPO. It provides a way for those unfamiliar with the ontology to search for and download plant phenology data of interest. It has also served as a proof of concept during ontology development, and as a means of checking these data.