Worm Community System

Caenorhabditis elegans is an unprepossessing critter, a millimeter long soil-dwelling worm that eats bacteria. Until recently, its main claim to fame has been that developmental biologists, who have adopted C. elegans as a model organism, understand its development more completely than that of any other multicelled creature. They have mapped out exactly where each of the worm's 959 cells lies and when each cell appears during the 3-day passage from fertilized ovum to fully functioning adult. Now, however, the tiny, transparent roundworm can add a second distinction to its c.v.: It is the subject of the most sophisticated and ambitious computer information network yet created, a network that offers a preview of what scientists in other fields can expect to encounter in coming years (see main text).

The Worm Community System (WCS) can be thought of as a "hyperlibrary," says Bruce Schatz, the University of Illinois scientist who developed it. At its heart is a computer network linking many C. elegans ..databases, formal and informal, so that a researcher can retrieve related information from many databases at once. The formal databases include gene descriptions, maps of the worm genome, DNA sequences, and journal articles--in effect, just about all "official" scientific knowledge on the worm. The informal databases fill in the gaps with such things as notes on experimental methods, lists of researchers, and the text of the Worm Breeders Gazette, the community's informal newsletter.

Much of this information was available through the Internet before Schatz appeared on the scene, but it was in isolated databases. A researcher would have to enter one database to retrieve a physical map, a second to pull out the DNA sequence of a particular gene, and a third to look for relevant literature on that gene--a clumsy, time-consuming procedure.

Windows on the worm. A search through the Worm Community System
pulls up various kinds of information from databases scattered around the country.

Schatz's scheme changes all that. Suppose you're interested in genes involved in the worm's sense of touch. You begin by entering "sensory," and the system finds every piece of literature that contains that word, displaying a one-line sum-mary of each. Next, you perform what Schatz calls a "group follow" to get all the genes mentioned in that literature. Each gene--or any set of genes--can then serve as the starting point for a new search. A user might, for example, ask for a display of a genetic map indicating the locations of all these genes. Or the user can choose one gene and get its sequence, its location on a physical map, or a list of genes that have related functions.

This ability to jump from one database to another depends on "links"--software connections between different pieces of information. Gene descriptions in one database, for instance, are linked to the locations of those genes on a physical map in another database. Schatz had to create the original links himself to get the WCS started, but ultimately it will be up to researchers using the system to add new links.

Users would create these links, as Schatz pictures it, each time they add their own information to the system. Suppose a researcher enters some data on a new gene, and he has noticed a functional similarity between his new find and a known worm gene. He can create a link between his gene and the older one and add a note explaining the similarity between them. The next time a scientist examines one of the genes and asks for related objects, the second gene will pop up.

"The way you get this giant interconnected space is to let the community do it," Schatz says, with everyone freely sharing information and ideas about how the information relates to what is already known. In this way far-flung researchers become part of a close-knit information community, building knowledge about a subject in much closer collaboration than was possible before.

But for that to happen, WCS has to catch on among worm biologists--and that's happening only slowly. Since it was set up 2 years ago, 25 of the 100 or so major worm labs around the world have signed on, and Schatz says another 25 have indicated that they plan to begin using it over the next year. At the Institute for Genomic Research in Gaithersburg, Maryland, Chris Fields says he finds Schatz's system particularly useful for browsing: "If I'm interested in this or that particular gene, then I look around." But like most other worm researchers, he says, he has used WCS only to get data out--not to put in new information to share with other scientists.

Fields says that's partly because creating new links was inconvenient in the first version of the software. A second version, released a few weeks ago, should lead to more use of this interactive function, says Schatz. But he thinks there's another reason fot the slow start. The system offers "a genuine revolution in how people are going to interact with knowledge," and it's going to take a while for researchers to get used to the idea of being members of an "electronic community," freely sharing their knowledge with other scientists in an ever-growing hyperlibrary. Nonetheless, the WCS shows enough promise that the recent NRC report on "national collaboratories" pointed to it as a proto-type for future electronic communities. Today C. elegans, tomorrow the world.


		...
.....	Caenorhabditis elegans is an unprepossessing critter, a millimeter long soil-dwelling worm that eats bacteria. Until recently, its main claim to fame has been that developmental biologists, who have adopted C. elegans as a model organism, understand its development more completely than that of any other multicelled creature. They have mapped out exactly where each of the worm's 959 cells lies and when each cell appears during the 3-day passage from fertilized ovum to fully functioning adult. Now, however, the tiny, transparent roundworm can add a second distinction to its c.v.: It is the subject of the most sophisticated and ambitious computer information network yet created, a network that offers a preview of what scientists in other fields can expect to encounter in coming years (see main text). The Worm Community System (WCS) can be thought of as a "hyperlibrary," says Bruce Schatz, the University of Illinois scientist who developed it. At its heart is a computer network linking many C. elegans ..databases, formal and informal, so that a researcher can retrieve related information from many databases at once. The formal databases include gene descriptions, maps of the worm genome, DNA sequences, and journal articles--in effect, just about all "official" scientific knowledge on the worm. The informal databases fill in the gaps with such things as notes on experimental methods, lists of researchers, and the text of the Worm Breeders Gazette, the community's informal newsletter. Much of this information was available through the Internet before Schatz appeared on the scene, but it was in isolated databases. A researcher would have to enter one database to retrieve a physical map, a second to pull out the DNA sequence of a particular gene, and a third to look for relevant literature on that gene--a clumsy, time-consuming procedure. Windows on the worm. A search through the Worm Community System pulls up various kinds of information from databases scattered around the country. Schatz's scheme changes all that. Suppose you're interested in genes involved in the worm's sense of touch. You begin by entering "sensory," and the system finds every piece of literature that contains that word, displaying a one-line sum-mary of each. Next, you perform what Schatz calls a "group follow" to get all the genes mentioned in that literature. Each gene--or any set of genes--can then serve as the starting point for a new search. A user might, for example, ask for a display of a genetic map indicating the locations of all these genes. Or the user can choose one gene and get its sequence, its location on a physical map, or a list of genes that have related functions. This ability to jump from one database to another depends on "links"--software connections between different pieces of information. Gene descriptions in one database, for instance, are linked to the locations of those genes on a physical map in another database. Schatz had to create the original links himself to get the WCS started, but ultimately it will be up to researchers using the system to add new links. Users would create these links, as Schatz pictures it, each time they add their own information to the system. Suppose a researcher enters some data on a new gene, and he has noticed a functional similarity between his new find and a known worm gene. He can create a link between his gene and the older one and add a note explaining the similarity between them. The next time a scientist examines one of the genes and asks for related objects, the second gene will pop up. "The way you get this giant interconnected space is to let the community do it," Schatz says, with everyone freely sharing information and ideas about how the information relates to what is already known. In this way far-flung researchers become part of a close-knit information community, building knowledge about a subject in much closer collaboration than was possible before. But for that to happen, WCS has to catch on among worm biologists--and that's happening only slowly. Since it was set up 2 years ago, 25 of the 100 or so major worm labs around the world have signed on, and Schatz says another 25 have indicated that they plan to begin using it over the next year. At the Institute for Genomic Research in Gaithersburg, Maryland, Chris Fields says he finds Schatz's system particularly useful for browsing: "If I'm interested in this or that particular gene, then I look around." But like most other worm researchers, he says, he has used WCS only to get data out--not to put in new information to share with other scientists. Fields says that's partly because creating new links was inconvenient in the first version of the software. A second version, released a few weeks ago, should lead to more use of this interactive function, says Schatz. But he thinks there's another reason fot the slow start. The system offers "a genuine revolution in how people are going to interact with knowledge," and it's going to take a while for researchers to get used to the idea of being members of an "electronic community," freely sharing their knowledge with other scientists in an ever-growing hyperlibrary. Nonetheless, the WCS shows enough promise that the recent NRC report on "national collaboratories" pointed to it as a proto-type for future electronic communities. Today C. elegans, tomorrow the world.	...
	.....	...
		...